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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, pentaerythritol propoxylate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 3.14 60.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.088 α = 90 b = 130.347 β = 90 c = 158.784 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 2013-08-29 M 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 2.08 46.89 99.6 0.067 19.23 62931 62911 2 28.176
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 2.08 2.21 98.8 0.323 0.365 5.18
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 MOLECULAR REPLACEMENT THROUGHOUT 2.08 46.89 62910 3146 99.6 0.1693 0.1671 0.1725 0.2126 0.2135 RANDOM 25.6116
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] 0.95 -1.5 0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.612 r_dihedral_angle_4_deg 15.184 r_dihedral_angle_3_deg 14.019 r_dihedral_angle_1_deg 6.178 r_mcangle_it 3.016 r_mcbond_it 2.163 r_mcbond_other 2.156 r_angle_refined_deg 1.993 r_angle_other_deg 0.927 r_chiral_restr 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.612 r_dihedral_angle_4_deg 15.184 r_dihedral_angle_3_deg 14.019 r_dihedral_angle_1_deg 6.178 r_mcangle_it 3.016 r_mcbond_it 2.163 r_mcbond_other 2.156 r_angle_refined_deg 1.993 r_angle_other_deg 0.927 r_chiral_restr 0.22 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_bond_other_d 0.005 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5476 Nucleic Acid Atoms Solvent Atoms 487 Heterogen Atoms 239
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection XDS data reduction XDS data scaling