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X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with a transition state analog of Glu-Glu
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, 1% (w/v) PEG 3350, 100 mM Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.34 63.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.405 α = 90 b = 130.797 β = 90 c = 159.14 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 MARMOSAIC 225 mm CCD 2006-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.000 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 1.67 50 97.4 0.091 23.4 10.9 119268 119268 -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 1.67 1.73 79.1 0.52 2.1 6.1 9667
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB entry 2oot 1.67 15 117320 1786 96.93 0.18377 0.18337 0.21142 0.2161 RANDOM 28.817
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] 0.9 -1.78 0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.437 r_dihedral_angle_4_deg 15.924 r_dihedral_angle_3_deg 14.438 r_sphericity_free 8.68 r_sphericity_bonded 8.602 r_dihedral_angle_1_deg 5.921 r_scangle_it 4.279 r_scbond_it 2.733 r_mcangle_it 1.784 r_angle_refined_deg 1.783
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.437 r_dihedral_angle_4_deg 15.924 r_dihedral_angle_3_deg 14.438 r_sphericity_free 8.68 r_sphericity_bonded 8.602 r_dihedral_angle_1_deg 5.921 r_scangle_it 4.279 r_scbond_it 2.733 r_mcangle_it 1.784 r_angle_refined_deg 1.783 r_mcbond_it 1.098 r_chiral_restr 0.13 r_bond_refined_d 0.021 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_rigid_bond_restr
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5529 Nucleic Acid Atoms Solvent Atoms 644 Heterogen Atoms 200
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling