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Structure of an inactive mutant of human glutamate carboxypeptidase II [GCPII(E424A)] in complex with N-acetyl-Asp-Glu (NAAG)
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, 0.5% (w/v) PEG 3350, 100 mM Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.3 62.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.063 α = 90 b = 129.801 β = 90 c = 159.589 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 2006-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.00 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 1.7 20 98.8 0.105 14.6 8.3 113478 113478 -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 1.7 1.76 96.9 0.393 3.5 6.5 11035
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 FOURIER SYNTHESIS THROUGHOUT pdb entry 2oot 1.71 15 111852 111852 1374 98.57 0.18465 0.18465 0.18429 0.1842 0.21309 0.208 RANDOM 30.376
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] 0.98 -2.23 1.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.067 r_dihedral_angle_4_deg 16.605 r_dihedral_angle_3_deg 14.089 r_sphericity_bonded 8.248 r_sphericity_free 7.396 r_dihedral_angle_1_deg 5.76 r_scangle_it 4.331 r_scbond_it 2.938 r_mcangle_it 1.92 r_angle_refined_deg 1.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.067 r_dihedral_angle_4_deg 16.605 r_dihedral_angle_3_deg 14.089 r_sphericity_bonded 8.248 r_sphericity_free 7.396 r_dihedral_angle_1_deg 5.76 r_scangle_it 4.331 r_scbond_it 2.938 r_mcangle_it 1.92 r_angle_refined_deg 1.87 r_mcbond_it 1.265 r_nbtor_refined 0.323 r_symmetry_vdw_refined 0.246 r_nbd_refined 0.212 r_symmetry_hbond_refined 0.194 r_xyhbond_nbd_refined 0.15 r_chiral_restr 0.145 r_metal_ion_refined 0.06 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 5546 Nucleic Acid Atoms Solvent Atoms 496 Heterogen Atoms 180
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling