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Crystal Structure of Glutamate Carboxypeptidase II in a complex with urea-based inhibitor
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 289 Tris-HCl, PEG 3350, pentaerythritol propoxylate, pH 8.0, temperature 289K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 3.18 61.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.543 α = 90 b = 130.297 β = 90 c = 159.864 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 120 IMAGE PLATE Mar2300 mirrors SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE OTHER 1.54
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 2.31 47.19 98.9 0.098 13.12 46307 2 33.309
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.31 2.45 97.6 0.47 0.534 3.64
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 MOLECULAR REPLACEMENT THROUGHOUT 2.31 47.19 46325 46307 2316 98.9 0.1785 0.1762 0.1764 0.2232 0.2208 RANDOM 29.0963
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] 0.4 -1.72 1.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.47 r_dihedral_angle_4_deg 18.483 r_dihedral_angle_3_deg 15.733 r_dihedral_angle_1_deg 6.569 r_mcangle_it 3.744 r_mcbond_it 2.518 r_mcbond_other 2.514 r_angle_refined_deg 2.033 r_angle_other_deg 0.912 r_chiral_restr 0.113
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.47 r_dihedral_angle_4_deg 18.483 r_dihedral_angle_3_deg 15.733 r_dihedral_angle_1_deg 6.569 r_mcangle_it 3.744 r_mcbond_it 2.518 r_mcbond_other 2.514 r_angle_refined_deg 2.033 r_angle_other_deg 0.912 r_chiral_restr 0.113 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5489 Nucleic Acid Atoms Solvent Atoms 285 Heterogen Atoms 167
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling