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A high resolution crystal structure of human glutamate carboxypeptidase II (GCPII) in a complex with DCFBD, 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 3.31 62.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.93 α = 90 b = 130.497 β = 90 c = 159.187 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 2006-07-24 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 1.69 30 99.5 0.094 14.8 6.5 116666 116666 -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 1.69 1.75 95.3 0.51 2.3 4.5 11057
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 1.69 15 114765 1730 99.02 0.17981 0.1795 0.19936 0.2136 RANDOM 28.483
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] 0.5 -1.96 1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.447 r_dihedral_angle_4_deg 14.464 r_dihedral_angle_3_deg 14.32 r_dihedral_angle_1_deg 10.318 r_sphericity_bonded 8.058 r_sphericity_free 6.133 r_scangle_it 4.097 r_scbond_it 2.744 r_angle_refined_deg 1.793 r_mcangle_it 1.793
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.447 r_dihedral_angle_4_deg 14.464 r_dihedral_angle_3_deg 14.32 r_dihedral_angle_1_deg 10.318 r_sphericity_bonded 8.058 r_sphericity_free 6.133 r_scangle_it 4.097 r_scbond_it 2.744 r_angle_refined_deg 1.793 r_mcangle_it 1.793 r_mcbond_it 1.178 r_symmetry_hbond_refined 0.381 r_nbtor_refined 0.321 r_symmetry_vdw_refined 0.31 r_nbd_refined 0.215 r_xyhbond_nbd_refined 0.156 r_chiral_restr 0.131 r_metal_ion_refined 0.07 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5529 Nucleic Acid Atoms Solvent Atoms 626 Heterogen Atoms 218
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling