☰ Navigation Tabs
X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with a inhibitor JHU2379
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BI1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 33% (v/v) pentaerythritol propoxylate PO/OH 5/4
2 % (w/v) PEG 3350
100 mM Tris-HCl, pH 8.0
Crystal Properties Matthews coefficient Solvent content 3.28 62.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.099 α = 90 b = 130.27 β = 90 c = 158.584 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 DECTRIS PILATUS3 6M 2016-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9796 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 1.63 30 98.7 0.059 0.065 0.999 16.13 5.22 128331 -3 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.63 1.73 98.2 0.906 1.002 0.865 2.11 5.28
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FOURIER SYNTHESIS THROUGHOUT 3BI1 1.63 30 -3 124566 3749 98.74 0.15494 0.15437 0.1592 0.17386 0.1792 RANDOM 33.723
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] 0.96 -2.28 1.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.775 r_dihedral_angle_4_deg 15.347 r_dihedral_angle_3_deg 13.678 r_long_range_B_refined 6.229 r_dihedral_angle_1_deg 6.039 r_scbond_it 2.275 r_mcangle_it 2.034 r_angle_refined_deg 1.754 r_mcbond_it 1.365 r_chiral_restr 0.126
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.775 r_dihedral_angle_4_deg 15.347 r_dihedral_angle_3_deg 13.678 r_long_range_B_refined 6.229 r_dihedral_angle_1_deg 6.039 r_scbond_it 2.275 r_mcangle_it 2.034 r_angle_refined_deg 1.754 r_mcbond_it 1.365 r_chiral_restr 0.126 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5516 Nucleic Acid Atoms Solvent Atoms 628 Heterogen Atoms 241
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing