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X-ray crystal structure of human biliverdin beta IX reductase in complex with NADP and BCT002104
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 protein solution: BLVRB at 18 mg/mL in 50 mM Bis-Tris, pH 6.5, 50 mM NaCl, 1 mM DTT, 1 mM NADP+
well solution: 0.1 M MES monohydrate pH 6.5, 10-12% (w/v) PEG 20,000, and 25% (v/v) MPD.
Crystallization droplets comprised 0.5 uL protein solution was mixed with 0.5 uL of well solution. BLVRB/NADP+ crystals were soaked for approximately 1 hour in a drop containing 2.5-5 mM BCT2104 (dissolved in 100% DMSO) and vitrified with 30% (v/v) glycerol as cryoprotectant.
Crystal Properties Matthews coefficient Solvent content 2.28 46.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.156 α = 90 b = 42.385 β = 107.41 c = 66.738 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 PIXEL DECTRIS EIGER X 9M KB bimorph mirrors 2024-05-25 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 1.72 31.841 99.8 0.13 0.152 0.078 0.995 6.1 3.8 21585 21.64
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 1.725 1.754 100 1.492 1.774 0.948 0.343 0.9 3.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.72 31.84 1.34 21462 1123 99.2 0.1962 0.1948 0.1949 0.2207 0.2211 26.12
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 13.6576 f_angle_d 1.0825 f_chiral_restr 0.0547 f_plane_restr 0.0074 f_bond_d 0.0064
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1529 Nucleic Acid Atoms Solvent Atoms 151 Heterogen Atoms 94
Software Software Software Name Purpose PHENIX refinement autoPROC data reduction PHASER phasing autoPROC data scaling