☰ Navigation Tabs
The crystal structure of an FMN-dependent NADH-azoreductase from Klebsiella pneumoniae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1V4B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6 291 0.1M MES pH 6.0, 25% PEG 8000, 0.2M calcium acetate
Crystal Properties Matthews coefficient Solvent content 2.6 52.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.668 α = 90 b = 97.323 β = 90.71 c = 77.534 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 2018-02-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97931 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.478 29.17 98.6 0.1 0.117 0.06 0.996 5.6 3.7 34876 51
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 2.48 2.61 91.5 0.642 0.777 0.432 0.736 3.1
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 1V4B 2.478 20 33185 1641 98.41 0.2396 0.2373 0.2398 0.2849 0.2835 RANDOM 48.043
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] 3.46 -4.88 -2.94 -0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.787 r_dihedral_angle_4_deg 17.082 r_dihedral_angle_3_deg 17.029 r_dihedral_angle_1_deg 6.751 r_angle_refined_deg 1.589 r_angle_other_deg 0.988 r_chiral_restr 0.076 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.787 r_dihedral_angle_4_deg 17.082 r_dihedral_angle_3_deg 17.029 r_dihedral_angle_1_deg 6.751 r_angle_refined_deg 1.589 r_angle_other_deg 0.988 r_chiral_restr 0.076 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6102 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms 93
Software Software Software Name Purpose REFMAC refinement SCALA data scaling MOLREP phasing PDB_EXTRACT data extraction MOSFLM data reduction