☰ Navigation Tabs
Crystal structure of Zn-dependent arginine carboxypeptidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2R8C PDB ENTRY 2R8C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 294 100mM Succinic acid pH 7.0, 15% PEG 3350, 10% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.98 58.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.42 α = 90 b = 146.583 β = 90 c = 255.963 γ = 90
Symmetry Space Group P 21 21 21
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 ADSC QUANTUM 315 MIRRORS 2007-06-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.15 50 94.8 0.13 0.1 3.7 4.2 230541 -0.5 20.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.23 87.4 0.52 0.54 0.8 2.7
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 2R8C 2.3 20 175832 5451 95.96 0.22767 0.22602 0.2233 0.27981 0.2745 RANDOM 48.347
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] -1.44 1.48 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.46 r_dihedral_angle_3_deg 21.232 r_dihedral_angle_4_deg 14.081 r_scangle_it 13.485 r_scbond_it 10.02 r_dihedral_angle_1_deg 9.968 r_mcangle_it 7.128 r_mcbond_it 5.189 r_angle_refined_deg 1.05 r_nbtor_refined 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.46 r_dihedral_angle_3_deg 21.232 r_dihedral_angle_4_deg 14.081 r_scangle_it 13.485 r_scbond_it 10.02 r_dihedral_angle_1_deg 9.968 r_mcangle_it 7.128 r_mcbond_it 5.189 r_angle_refined_deg 1.05 r_nbtor_refined 0.29 r_xyhbond_nbd_refined 0.149 r_nbd_refined 0.127 r_symmetry_hbond_refined 0.106 r_chiral_restr 0.104 r_symmetry_vdw_refined 0.089 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 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_refined 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 24048 Nucleic Acid Atoms Solvent Atoms 572 Heterogen Atoms 194
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling