☰ Navigation Tabs
Putative oxidoreductase from Escherichia coli str. K-12
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DML
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 28% PEG 400, 0.2M CaCl2, 0.1M Hepes buffer
Crystal Properties Matthews coefficient Solvent content 2.14 42.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.819 α = 82.59 b = 72.21 β = 87.03 c = 119.945 γ = 67.82
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 210r 2019-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.9792 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.36 48.14 88.3 0.041 0.052 0.031 16.7 2.5 320625
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.36 1.38 43.2 0.516 0.669 0.421 0.591 1.44 2.1
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 4DML 1.36 48.14 304841 15748 88.12 0.1255 0.1232 0.1234 0.1692 0.1696 RANDOM 19.197
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] 0.29 -0.37 0.36 -0.61 -0.36 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.341 r_dihedral_angle_4_deg 16.999 r_dihedral_angle_3_deg 12.703 r_dihedral_angle_1_deg 6.995 r_rigid_bond_restr 2.046 r_angle_refined_deg 1.589 r_angle_other_deg 1.504 r_chiral_restr 0.088 r_bond_refined_d 0.01 r_gen_planes_refined 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.341 r_dihedral_angle_4_deg 16.999 r_dihedral_angle_3_deg 12.703 r_dihedral_angle_1_deg 6.995 r_rigid_bond_restr 2.046 r_angle_refined_deg 1.589 r_angle_other_deg 1.504 r_chiral_restr 0.088 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14289 Nucleic Acid Atoms Solvent Atoms 1801 Heterogen Atoms 40
Software Software Software Name Purpose HKL-3000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 phasing