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Human biliverdin IX beta reductase in complex with NADP in space group P1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9C16
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 0.1 M MES pH 6.5, 12% (w/v) PEG20000, 25% (v/v) MPD, 1 mM NADP+
Crystal Properties Matthews coefficient Solvent content 2.1 41.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.94 α = 84.11 b = 41.977 β = 87.24 c = 60.212 γ = 63.66
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 9M KB bimorph 2024-04-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.9201 NSLS-II 17-ID-1
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 1.9 31.88 97.8 0.196 0.231 0.12 0.988 4.3 3.6 28264 24.69
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 1.9 1.93 1.996 2.33 1.196 0.367 0.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 9C16 1.9 31.88 1.96 28084 1640 97.19 0.2071 0.2056 0.2053 0.2292 0.2288 28.73
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.3993 f_angle_d 0.9796 f_chiral_restr 0.0553 f_plane_restr 0.0071 f_bond_d 0.0069
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3070 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms 96
Software Software Software Name Purpose PHENIX refinement autoPROC data reduction PHASER phasing XDS data scaling