1HE3

Human biliverdin IX beta reductase: NADP/mesobiliverdin IV alpha ternary complex


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.530% PEG 3350, 0.2 M AMMONIUM SULFATE, 0.1 M SODIUM CACODYLATE PH 6.5. NADP ADDED TO A FINAL CONCENTRATION OF 2.5 MM
Crystal Properties
Matthews coefficientSolvent content
2.340.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.2α = 90
b = 49.4β = 90
c = 107.1γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray1002000-05-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-3ESRFID14-3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.444.798.60.084.13.842097
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.4898.60.183

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1HDO1.42042030211598.30.1380.1320.181RANDOM
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]
Coordinate Error
Structure Solution MethodRefinement High ResolutionRefinement Low Resolution
131860.38
RMS Deviations
KeyRefinement Restraint Deviation
s_approx_iso_adps0.08
s_similar_adp_cmpnt0.028
s_angle_d0.027
s_non_zero_chiral_vol0.027
s_from_restr_planes0.026
s_zero_chiral_vol0.019
s_anti_bump_dis_restr0.015
s_bond_d0.011
s_rigid_bond_adp_cmpnt0.004
s_similar_dist
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1536
Nucleic Acid Atoms
Solvent Atoms289
Heterogen Atoms91

Software

Software
Software NamePurpose
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing