what you may have is two alternate conformations - i.e. your current one and one with the CD-NE bond rotated 180 degrees. Your density looks like an average between these two (to me at least and adaict from your image).
Mark J van Raaij Lab 20B Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 15 Apr 2013, at 12:12, Kavyashree Manjunath wrote: > Sir, > > I have examined the density. Its extremely clear. I am attaching > the 2FoFc map map of this residue. As I mentioned previously, The > side chain density was conformed by deleting it and refining. > > > Thank you > Regards > Kavya > >> Dear Kavya, >> >> I would examine the electron density of your Arginine. It may be present >> in two alternative conformations and you may have fitted the Arginine in >> the middle, e.g. with the NH1 in one conformation and the NH2 in the >> other. >> >> The Arginine may also just be incorrectly fitted. Using Coot with "Auto >> Fit Rotatmer" and "Real Space Refine Zone" you might be able to correct >> it. Just using "Regularize Zone" on the Arginine might give hints how the >> Arginine got distorted. However, before running another round of >> refinement, it needs to be fitted back in electron density. >> >> Best, >> Herman >> >> -----Original Message----- >> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of >> Kavyashree Manjunath >> Sent: Monday, April 15, 2013 9:41 AM >> To: CCP4BB@JISCMAIL.AC.UK >> Subject: Re: [ccp4bb] Angle restraints >> >> Sir, >> >> I used RCSB validation server. Deviations are as given below - >> Deviation Resi AT1 - AT2 - AT3 Bond Dict Std >> Angle Value Dev >> -------------------------------------------------------------- >> 3.2 ARG NE - CZ - NH1 123.5 120.3 0.5 >> -3.4 ARG NE - CZ - NH2 116.9 120.3 0.5 >> >> >> Thus its more than 6 sigmas in both the cases. Its not an outlier. >> zANGL is 0.628 and Rms BondAngle is 1.4077. >> would you suggest me to ignore this deviation? But will it not be a >> problem during PDB submission? >> What is the reason I am getting a deviation like this? Should I reduce the >> weighing term further down? >> >> Thanking you >> Regards >> Kavya >>> Hi Kavya, >>> >>> Which validation program did you use? How big is the deviation (in >>> sigma values)? Is it the only outlier? What is your overall bond angle >>> rmsZ? >>> >>> Using external restraints is a bit over the top here, especially if it >>> is the only outlier. If your rmsZ is high (close to or over 1) then >>> you may want to try tighter geometric restraints overall. >>> In a normal distribution it is not surprising to find a 'true' >>> outlier, so if your structure is large you need to worry less. >>> >>> Cheers, >>> Robbie >>> >>> Sent from my Windows Phone >>> ________________________________ >>> From: Kavyashree Manjunath >>> Sent: 2013-04-15 07:13 >>> To: CCP4BB@JISCMAIL.AC.UK >>> Subject: [ccp4bb] Angle restraints >>> >>> Dear users, >>> >>> Validation of a structure showed a deviation in the angle between >>> atoms NH1-CZ-NE and NH2-CZ-NE in the arginine residue. Several trials >>> of modification of the orientation failed to solve this problem. I >>> also confirmed by deleting the side chain and refining, it confirmed >>> the presence of complete side chain. So I proceeded to use external >>> restraints for these two angles in refmac5 (version 5.6.0117). >>> >>> The keyword was as follows - >>> external angle first chain A residue 93 atom NE next chain A residue >>> 93 atom CZ next chain A residue 93 atom NH1 value 120.3 sigma 0.5 >>> external angle first chain A residue 93 atom NH2 next chain A residue >>> 93 atom CZ next chain A residue 93 atom NE value 120.3 sigma 0.5 >>> >>> Still there is no change in the angle, it continues to have the same >>> deviation. >>> >>> So kindly suggest whether there is any error in the keyword provided >>> or other way to handle this problem. >>> >>> Thanking you >>> Regards >>> Kavya >>> >>> >>> -- >>> This message has been scanned for viruses and dangerous content by >>> MailScanner, and is believed to be clean. >>> >>> -- >>> This message has been scanned for viruses and dangerous content by >>> MailScanner, and is believed to be clean. >>> >>> >> >> >> >> -- >> This message has been scanned for viruses and dangerous content by >> MailScanner, and is believed to be clean. >> >> -- >> This message has been scanned for viruses and >> dangerous content by MailScanner, and is >> believed to be clean. >> >> > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > <Arg.png>
