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A high resolution crystal structure of human glutamate carboxypeptidase II (GCPII) in a complex with DCMC, a urea-based inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 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 3.29 62.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.79 α = 90 b = 129.694 β = 90 c = 159.299 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 300 mm CCD 2007-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.000 APS 22-ID
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 1.75 30 99.6 0.07 21.5 6.8 105078 105078 -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 1.75 1.81 96.9 0.49 2.4 2.4 10129
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 2oot 1.75 15 103375 1550 99.1 0.17012 0.16962 0.20441 0.2099 RANDOM 28.078
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] 0.82 -1.85 1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.52 r_dihedral_angle_3_deg 14.832 r_dihedral_angle_4_deg 14.655 r_dihedral_angle_1_deg 10.869 r_sphericity_bonded 7.258 r_sphericity_free 5.772 r_scangle_it 4.254 r_scbond_it 2.88 r_angle_refined_deg 1.924 r_mcangle_it 1.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.52 r_dihedral_angle_3_deg 14.832 r_dihedral_angle_4_deg 14.655 r_dihedral_angle_1_deg 10.869 r_sphericity_bonded 7.258 r_sphericity_free 5.772 r_scangle_it 4.254 r_scbond_it 2.88 r_angle_refined_deg 1.924 r_mcangle_it 1.87 r_mcbond_it 1.228 r_nbtor_refined 0.323 r_symmetry_vdw_refined 0.263 r_symmetry_hbond_refined 0.234 r_nbd_refined 0.219 r_xyhbond_nbd_refined 0.172 r_chiral_restr 0.14 r_metal_ion_refined 0.082 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_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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5499 Nucleic Acid Atoms Solvent Atoms 617 Heterogen Atoms 211
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling