7ER9

Crystal structure of human Biliverdin IX-beta reductase B with Febuxostat (TEI)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HE5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5291.151.9-2.0M Ammonium sulfate, 0.1M Bis-tris (pH 6.5)
Crystal Properties
Matthews coefficientSolvent content
2.1943.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.041α = 90
b = 117.352β = 90
c = 41.606γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-10-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 11C0.97942PAL/PLS11C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.44947.7396.650.066650.99915.439.26979413.99
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.4491.5010.39430.826

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1HE51.4547.731.4569792199996.650.15620.15520.190424.35
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
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.99
f_angle_d1.2261
f_chiral_restr0.0859
f_bond_d0.0107
f_plane_restr0.0071
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3116
Nucleic Acid Atoms
Solvent Atoms463
Heterogen Atoms160

Software

Software
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
HKL-2000data scaling
PHENIXmodel building
PHASERphasing
HKL-2000data reduction