2YVF

Crystal structure of ferredoxin reductase BPHA4 (hydroquinone)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.42932M SODIUM FORMATE, 0.1M SODIUM ACETATE, pH 5.40, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6954.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.597α = 90
b = 97.597β = 90
c = 169.463γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102005-06-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12APhoton FactoryAR-NW12A

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
11.61595.90.06721.5411.660816
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)
11.61.6894.40.6853.17.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONDIFFERENCE FOURIERTHROUGHOUT1.6155768330361000.1890.1880.214RANDOM29.59
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]
-0.36-0.18-0.360.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.699
r_dihedral_angle_4_deg16.397
r_dihedral_angle_3_deg12.823
r_dihedral_angle_1_deg5.308
r_scangle_it3.128
r_scbond_it1.978
r_angle_refined_deg1.42
r_mcangle_it1.168
r_mcbond_it0.754
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.699
r_dihedral_angle_4_deg16.397
r_dihedral_angle_3_deg12.823
r_dihedral_angle_1_deg5.308
r_scangle_it3.128
r_scbond_it1.978
r_angle_refined_deg1.42
r_mcangle_it1.168
r_mcbond_it0.754
r_nbtor_refined0.309
r_symmetry_vdw_refined0.239
r_symmetry_hbond_refined0.212
r_nbd_refined0.2
r_xyhbond_nbd_refined0.139
r_chiral_restr0.084
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2963
Nucleic Acid Atoms
Solvent Atoms207
Heterogen Atoms112

Software

Software
Software NamePurpose
XTALVIEWrefinement
REFMACrefinement
ADSCdata collection
XDSdata scaling