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A High Resolution Structure of Ligand-free Human Glutamate Carboxypeptidase II
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2C6G PDB ENTRY 2C6G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 33% (v/v) pentaerythritol propoxylate PO/OH 5/4, 13% (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 62.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.759 α = 90 b = 130.128 β = 90 c = 158.874 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 2006-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.0000 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 1.65 30 98.7 0.082 19.7 9.8 126082 126082 -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 1.65 1.71 91.6 0.598 2.6 6.5 11591
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 PDB ENTRY 2C6G 1.64 30 121530 3784 97.95 0.20693 0.20623 0.2039 0.22841 0.2253 RANDOM 29.292
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] 1.03 -1.72 0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.207 r_dihedral_angle_4_deg 15.539 r_dihedral_angle_3_deg 15.063 r_sphericity_free 9.952 r_sphericity_bonded 7.383 r_dihedral_angle_1_deg 5.958 r_scangle_it 4.155 r_scbond_it 2.772 r_mcangle_it 1.824 r_angle_refined_deg 1.795
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.207 r_dihedral_angle_4_deg 15.539 r_dihedral_angle_3_deg 15.063 r_sphericity_free 9.952 r_sphericity_bonded 7.383 r_dihedral_angle_1_deg 5.958 r_scangle_it 4.155 r_scbond_it 2.772 r_mcangle_it 1.824 r_angle_refined_deg 1.795 r_mcbond_it 1.202 r_nbtor_refined 0.319 r_symmetry_vdw_refined 0.24 r_nbd_refined 0.219 r_xyhbond_nbd_refined 0.174 r_symmetry_hbond_refined 0.156 r_chiral_restr 0.123 r_metal_ion_refined 0.06 r_bond_refined_d 0.019 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5459 Nucleic Acid Atoms Solvent Atoms 560 Heterogen Atoms 166
Software Software Software Name Purpose REFMAC refinement MAR345 data collection HKL-2000 data reduction HKL-2000 data scaling