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X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with a phosphoramidate inhibitor JRB-4-81
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 288 34% (v/v) pentaerythritol propoxylate PO/OH 5/4, 2 % (w/v) PEG 3350, and 100 mM Tris-HCl, pH 8.0
Crystal Properties Matthews coefficient Solvent content 3.31 62.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.505 α = 90 b = 130.487 β = 90 c = 158.939 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 CCD RAYONIX MX-225 2013-02-14 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 1.75 29.51 99.8 0.06 21.6 5.8 105804
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.86 99.4 5.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.75 29.51 -3 100472 5288 100 0.16403 0.16279 0.1629 0.18723 0.1871 RANDOM 26.414
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] 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.363 r_dihedral_angle_4_deg 16.305 r_dihedral_angle_3_deg 13.094 r_dihedral_angle_1_deg 5.809 r_scangle_it 4.355 r_scbond_it 2.662 r_angle_refined_deg 1.692 r_mcangle_it 1.628 r_mcbond_it 0.953 r_chiral_restr 0.135
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.363 r_dihedral_angle_4_deg 16.305 r_dihedral_angle_3_deg 13.094 r_dihedral_angle_1_deg 5.809 r_scangle_it 4.355 r_scbond_it 2.662 r_angle_refined_deg 1.692 r_mcangle_it 1.628 r_mcbond_it 0.953 r_chiral_restr 0.135 r_bond_refined_d 0.019 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_other r_long_range_B_refined 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 5503 Nucleic Acid Atoms Solvent Atoms 603 Heterogen Atoms 217
Software Software Software Name Purpose REFMAC refinement DENZO data reduction XSCALE data scaling