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The high resolution structure of human glutamate carboxypeptidase III (GCPIII/NAALADase II) 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 2OR4 PDB entry 2OR4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.1M HEPES-Na, 10% (w/v) PEG6000, 5% (v/v) MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.95 58.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.731 α = 90 b = 104.086 β = 108.19 c = 77.634 γ = 90
Symmetry Space Group C 1 2 1
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-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 1.29 30 97.8 0.092 6.6 227958 227958 -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 1.29 1.34 79.8 0.469 1.9 3 18560
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 FOURIER SYNTHESIS THROUGHOUT PDB entry 2OR4 1.29 25 225644 2292 98.74 0.13104 0.13087 0.1399 0.14727 0.1464 RANDOM 18.382
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] 0.03 0.25 0.35 -0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.741 r_dihedral_angle_4_deg 18.777 r_dihedral_angle_3_deg 13.484 r_sphericity_free 9.96 r_dihedral_angle_1_deg 5.86 r_sphericity_bonded 5.474 r_scangle_it 5.186 r_scbond_it 3.568 r_mcangle_it 2.701 r_rigid_bond_restr 2.058
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.741 r_dihedral_angle_4_deg 18.777 r_dihedral_angle_3_deg 13.484 r_sphericity_free 9.96 r_dihedral_angle_1_deg 5.86 r_sphericity_bonded 5.474 r_scangle_it 5.186 r_scbond_it 3.568 r_mcangle_it 2.701 r_rigid_bond_restr 2.058 r_mcbond_it 1.862 r_angle_refined_deg 1.83 r_chiral_restr 0.125 r_bond_refined_d 0.017 r_gen_planes_refined 0.014 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5504 Nucleic Acid Atoms Solvent Atoms 861 Heterogen Atoms 94
Software Software Software Name Purpose MAR345dtb data collection Coot model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling