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Structure of inactive GCPII mutant in complex with beta-citryl glutamate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NPG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 288.15 33% (v/v) pentaerythritol propoxylate PO/OH 5/4 (Hampton Research, Aliso Viejo, Ca, USA), 1.5% (w/v) PEG 3350 (Merck KGaA, Darmstadt, Germany) and 0.10 M Tris-HCl (Merck KGaA), pH 8.0
Crystal Properties Matthews coefficient Solvent content 3.35 63.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.901 α = 90 b = 130.923 β = 90 c = 159.136 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL PSI PILATUS 6M 2014-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.85 30 98.8 0.081 0.081 13.29 4.51 89051 -3 35.174
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.96 97.1 0.94 0.941 1.96 4.43
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4NPG 1.85 30 84513 4444 99.04 0.1565 0.1552 0.1669 0.1814 0.1912 RANDOM 40.583
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.58 -1.69 1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.923 r_dihedral_angle_4_deg 15.467 r_sphericity_free 13.418 r_dihedral_angle_3_deg 12.862 r_sphericity_bonded 9.865 r_dihedral_angle_1_deg 6.176 r_mcangle_it 1.695 r_angle_refined_deg 1.69 r_mcbond_it 1.033 r_mcbond_other 1.033
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.923 r_dihedral_angle_4_deg 15.467 r_sphericity_free 13.418 r_dihedral_angle_3_deg 12.862 r_sphericity_bonded 9.865 r_dihedral_angle_1_deg 6.176 r_mcangle_it 1.695 r_angle_refined_deg 1.69 r_mcbond_it 1.033 r_mcbond_other 1.033 r_angle_other_deg 1.02 r_chiral_restr 0.095 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_gen_planes_other 0.004 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5492 Nucleic Acid Atoms Solvent Atoms 562 Heterogen Atoms 223
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling MOLREP phasing PDB_EXTRACT data extraction XDS data reduction Coot model building