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X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with a inhibitor RNA 1-79-1
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 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 3.37 63.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.258 α = 90 b = 131.376 β = 90 c = 159.874 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 PILATUS3 2M 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) 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 1.81 50 98.8 0.073 0.079 0.999 16.17 6.7 96547 -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 1.81 1.92 93.4 0.849 0.93 0.871 1.94 6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 3BI1 1.81 47.26 94359 2099 98.67 0.15045 0.14983 0.17756 0.1801 RANDOM 43.915
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] 1.15 -2.58 1.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.077 r_dihedral_angle_4_deg 16.041 r_dihedral_angle_3_deg 14.757 r_dihedral_angle_1_deg 6.663 r_long_range_B_refined 5.442 r_long_range_B_other 5.442 r_scangle_other 3.806 r_mcangle_it 2.548 r_mcangle_other 2.548 r_scbond_it 2.507
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.077 r_dihedral_angle_4_deg 16.041 r_dihedral_angle_3_deg 14.757 r_dihedral_angle_1_deg 6.663 r_long_range_B_refined 5.442 r_long_range_B_other 5.442 r_scangle_other 3.806 r_mcangle_it 2.548 r_mcangle_other 2.548 r_scbond_it 2.507 r_scbond_other 2.507 r_mcbond_it 1.824 r_mcbond_other 1.824 r_angle_refined_deg 1.802 r_angle_other_deg 1.357 r_chiral_restr 0.112 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 5546 Nucleic Acid Atoms Solvent Atoms 427 Heterogen Atoms 321
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling REFMAC phasing Coot model building