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X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with a inhibitor RNA 2-19-1
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 34 % (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 3.38 63.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.296 α = 90 b = 131.658 β = 90 c = 160.019 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 90 PIXEL DECTRIS PILATUS 6M 2018-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.918 BESSY 14.2
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 2.09 50 99.2 0.12 12.58 6.7 63204
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 2.09 2.22 97 0.943 1.97 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 FOURIER SYNTHESIS THROUGHOUT 3BI1 2.09 47.3 61201 2100 99.36 0.16186 0.16038 0.175 0.2044 0.2123 RANDOM 55.506
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] 1.89 -3.35 1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.748 r_dihedral_angle_4_deg 17.017 r_dihedral_angle_3_deg 15.781 r_dihedral_angle_1_deg 6.674 r_long_range_B_refined 6.518 r_long_range_B_other 6.518 r_scangle_other 5.324 r_scbond_it 3.9 r_scbond_other 3.9 r_mcangle_it 3.844
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.748 r_dihedral_angle_4_deg 17.017 r_dihedral_angle_3_deg 15.781 r_dihedral_angle_1_deg 6.674 r_long_range_B_refined 6.518 r_long_range_B_other 6.518 r_scangle_other 5.324 r_scbond_it 3.9 r_scbond_other 3.9 r_mcangle_it 3.844 r_mcangle_other 3.843 r_mcbond_it 3.058 r_mcbond_other 3.058 r_angle_refined_deg 1.834 r_angle_other_deg 1.167 r_chiral_restr 0.085 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5529 Nucleic Acid Atoms Solvent Atoms 395 Heterogen Atoms 208
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling Coot model building REFMAC phasing