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X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with a hydroxamate inhibitor JHU241
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 3.28 62.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.191 α = 90 b = 130.459 β = 90 c = 157.196 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 2013-04-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.91841 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 1.8 50 99.7 0.062 20.24 5.83 95135 -3 -3
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 1.8 1.91 99.3 0.683 2.72
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.8 44.82 90374 4757 100 0.1758 0.1743 0.1752 0.2049 0.2049 RANDOM 31.965
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] 1.52 -2.7 1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.695 r_dihedral_angle_4_deg 15.043 r_dihedral_angle_3_deg 14.602 r_dihedral_angle_1_deg 6.099 r_scangle_it 4.471 r_scbond_it 2.83 r_angle_refined_deg 1.739 r_mcangle_it 1.713 r_mcbond_it 1.016 r_chiral_restr 0.137
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.695 r_dihedral_angle_4_deg 15.043 r_dihedral_angle_3_deg 14.602 r_dihedral_angle_1_deg 6.099 r_scangle_it 4.471 r_scbond_it 2.83 r_angle_refined_deg 1.739 r_mcangle_it 1.713 r_mcbond_it 1.016 r_chiral_restr 0.137 r_bond_refined_d 0.02 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5464 Nucleic Acid Atoms Solvent Atoms 364 Heterogen Atoms 190
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction XSCALE data scaling MAR345dtb data collection