3LZW

Crystal structure of ferredoxin-NADP+ oxidoreductase from bacillus subtilis (form I)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52930.1M HEPES buffer (pH 7.5), 30% 1,2-propanediol, 20% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.346.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.9α = 90
b = 135.724β = 90
c = 39.191γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU JUPITER 2102008-07-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL38B11.0000SPring-8BL38B1

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
11.826.8799.90.071732363
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)
1.81.8699.50.3886.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2ZBW1.826.873070716021000.170230.168850.19645RANDOM24.212
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]
0.17-0.710.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.807
r_dihedral_angle_3_deg12.417
r_dihedral_angle_4_deg8.977
r_dihedral_angle_1_deg5.3
r_scangle_it1.976
r_angle_refined_deg1.253
r_scbond_it1.237
r_angle_other_deg0.799
r_mcangle_it0.796
r_mcbond_it0.422
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.807
r_dihedral_angle_3_deg12.417
r_dihedral_angle_4_deg8.977
r_dihedral_angle_1_deg5.3
r_scangle_it1.976
r_angle_refined_deg1.253
r_scbond_it1.237
r_angle_other_deg0.799
r_mcangle_it0.796
r_mcbond_it0.422
r_symmetry_vdw_other0.231
r_nbd_refined0.195
r_nbd_other0.176
r_nbtor_refined0.174
r_xyhbond_nbd_refined0.137
r_chiral_restr0.133
r_symmetry_hbond_refined0.131
r_symmetry_vdw_refined0.117
r_metal_ion_refined0.107
r_mcbond_other0.091
r_nbtor_other0.081
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2570
Nucleic Acid Atoms
Solvent Atoms240
Heterogen Atoms103

Software

Software
Software NamePurpose
BSSdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling