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A high resolution crystal structure of human glutamate carboxypeptidase II in complex with quisqualic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OOT PDB ENTRY 2OOT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 33% (v/v) pentaerythritol propoxylate PO/OH 5/4, 13% (w/v) PEG 3350, 100 mM Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.32 62.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.007 α = 90 b = 130.437 β = 90 c = 159.508 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 MAR CCD 225 mm 2006-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.0000 APS 22-BM
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 1.62 50 96.7 0.07 28.2 11 129603 129603 -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 1.62 1.68 74.8 0.465 2.7 5.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION Rigid body THROUGHOUT PDB ENTRY 2OOT 1.62 30 123053 6521 96.59 0.18593 0.1842 0.1811 0.21908 0.2143 RANDOM 27.218
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] 0.94 -1.85 0.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.264 r_dihedral_angle_3_deg 14.406 r_dihedral_angle_4_deg 13.007 r_sphericity_free 7.115 r_dihedral_angle_1_deg 5.774 r_scangle_it 3.989 r_scbond_it 2.681 r_angle_refined_deg 1.939 r_mcangle_it 1.797 r_mcbond_it 1.222
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.264 r_dihedral_angle_3_deg 14.406 r_dihedral_angle_4_deg 13.007 r_sphericity_free 7.115 r_dihedral_angle_1_deg 5.774 r_scangle_it 3.989 r_scbond_it 2.681 r_angle_refined_deg 1.939 r_mcangle_it 1.797 r_mcbond_it 1.222 r_nbtor_refined 0.32 r_symmetry_vdw_refined 0.234 r_nbd_refined 0.228 r_symmetry_hbond_refined 0.218 r_xyhbond_nbd_refined 0.168 r_chiral_restr 0.137 r_metal_ion_refined 0.057 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5486 Nucleic Acid Atoms Solvent Atoms 874 Heterogen Atoms 193
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection HKL-2000 data reduction HKL-2000 data scaling