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Structure of human glutamate carboxypeptidase II (GCPII) in complex with L-serine-O-sulfate
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 3% (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 62.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.617 α = 90 b = 130.22 β = 90 c = 158.975 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 IMAGE PLATE MAR scanner 345 mm plate 2006-12-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
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 2.1 30 98.9 0.097 15.4 4.8 60304 60304 -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 2.1 2.18 98.4 0.505 3.7 4.8 5928
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 Difference Fourier THROUGHOUT 2OOT 2.11 30 57236 3061 98.56 0.17622 0.17424 0.1713 0.21214 0.2095 RANDOM 29.73
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] 1.47 -2.21 0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.892 r_dihedral_angle_4_deg 16.406 r_dihedral_angle_3_deg 14.712 r_dihedral_angle_1_deg 6.431 r_scangle_it 4.06 r_scbond_it 2.808 r_angle_refined_deg 1.803 r_mcangle_it 1.769 r_mcbond_it 1.127 r_nbtor_refined 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.892 r_dihedral_angle_4_deg 16.406 r_dihedral_angle_3_deg 14.712 r_dihedral_angle_1_deg 6.431 r_scangle_it 4.06 r_scbond_it 2.808 r_angle_refined_deg 1.803 r_mcangle_it 1.769 r_mcbond_it 1.127 r_nbtor_refined 0.316 r_symmetry_vdw_refined 0.242 r_nbd_refined 0.212 r_xyhbond_nbd_refined 0.167 r_symmetry_hbond_refined 0.161 r_chiral_restr 0.125 r_metal_ion_refined 0.105 r_bond_refined_d 0.021 r_gen_planes_refined 0.009 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_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5529 Nucleic Acid Atoms Solvent Atoms 510 Heterogen Atoms 191
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection HKL-2000 data reduction HKL-2000 data scaling