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Varying binding modes of inhibitors and structural differences in the binding pockets of different gamma-glutamyltranspeptidases
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NQO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 PEG3350, 0.1M TRIS
Crystal Properties Matthews coefficient Solvent content 2.82 56.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.777 α = 90 b = 112.006 β = 90.79 c = 91.854 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARRESEARCH 2010-04-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.000 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.49 91.84 99.2 0.07 16.6 3.7 176874
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.49 1.55 98.5 0.51 3.7
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 2NQO 1.49 91.8 170766 4718 99.21 0.1449 0.1438 0.1532 0.1837 0.1913 RANDOM 13.238
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] -0.49 0.53 0.84 -0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.078 r_dihedral_angle_4_deg 16.768 r_dihedral_angle_3_deg 12.107 r_sphericity_free 8.961 r_dihedral_angle_1_deg 6.192 r_scangle_it 5.766 r_sphericity_bonded 4.463 r_scbond_it 4.219 r_mcangle_it 3.114 r_mcbond_it 2.289
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.078 r_dihedral_angle_4_deg 16.768 r_dihedral_angle_3_deg 12.107 r_sphericity_free 8.961 r_dihedral_angle_1_deg 6.192 r_scangle_it 5.766 r_sphericity_bonded 4.463 r_scbond_it 4.219 r_mcangle_it 3.114 r_mcbond_it 2.289 r_rigid_bond_restr 2.009 r_angle_refined_deg 1.221 r_mcbond_other 1.211 r_angle_other_deg 0.871 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8142 Nucleic Acid Atoms Solvent Atoms 961 Heterogen Atoms 192
Software Software Software Name Purpose REFMAC refinement MOLREP phasing XDS data reduction XSCALE data scaling