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Structure of the biliverdin reductase Rv2074 from Mycobacterium tuberculosis in complex with F420
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ASF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 292.15 27% PEG3350, 0.2M MgCl2, 0.1 M BisTris
Crystal Properties Matthews coefficient Solvent content 2.28 45.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.756 α = 90 b = 88.62 β = 90 c = 98.625 γ = 90
Symmetry Space Group P 2 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 315r 2015-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.65 65.92 100 0.181 0.994 9.3 7.1 65830
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 1.68 99.9 1.261 6.7
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 2ASF 1.65 65.92 62534 3266 99.96 0.1801 0.1782 0.1897 0.2166 0.2263 RANDOM 20.763
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] -0.07 -0.04 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.052 r_dihedral_angle_4_deg 18.103 r_dihedral_angle_3_deg 12.345 r_dihedral_angle_1_deg 7.556 r_mcangle_it 2.924 r_mcbond_it 2.014 r_mcbond_other 2.007 r_angle_refined_deg 1.962 r_angle_other_deg 1.682 r_chiral_restr 0.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.052 r_dihedral_angle_4_deg 18.103 r_dihedral_angle_3_deg 12.345 r_dihedral_angle_1_deg 7.556 r_mcangle_it 2.924 r_mcbond_it 2.014 r_mcbond_other 2.007 r_angle_refined_deg 1.962 r_angle_other_deg 1.682 r_chiral_restr 0.112 r_bond_refined_d 0.019 r_gen_planes_refined 0.015 r_bond_other_d 0.01 r_gen_planes_other 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4034 Nucleic Acid Atoms Solvent Atoms 654 Heterogen Atoms 252
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing PDB_EXTRACT data extraction XDS data reduction