☰ Navigation Tabs
The high resolution structure of human glutamate carboxypeptidase III (GCPIII/NAALADase II) in complex with quisqualic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FED PDB entry 3FED
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.1 M 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 2.94 58.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.985 α = 90 b = 103.69 β = 108.27 c = 77.611 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 325 mm CCD 2006-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.2759 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 1.56 50 99.2 0.049 3.6 130199 130199 -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 1.56 1.62 97 0.261 4.9 3.5 12705
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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3FED 1.56 25 128862 1313 99.3 0.14966 0.14933 0.1506 0.18438 0.1873 RANDOM 17.561
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] 0.12 0.21 -0.12 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.021 r_dihedral_angle_4_deg 18.757 r_dihedral_angle_3_deg 13.155 r_dihedral_angle_1_deg 5.846 r_scangle_it 4.042 r_scbond_it 2.532 r_angle_refined_deg 1.858 r_mcangle_it 1.664 r_mcbond_it 1.002 r_chiral_restr 0.132
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.021 r_dihedral_angle_4_deg 18.757 r_dihedral_angle_3_deg 13.155 r_dihedral_angle_1_deg 5.846 r_scangle_it 4.042 r_scbond_it 2.532 r_angle_refined_deg 1.858 r_mcangle_it 1.664 r_mcbond_it 1.002 r_chiral_restr 0.132 r_bond_refined_d 0.019 r_gen_planes_refined 0.012 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5496 Nucleic Acid Atoms Solvent Atoms 828 Heterogen Atoms 87
Software Software Software Name Purpose MAR345dtb data collection XFIT data reduction REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling