3LZX

Crystal structure of ferredoxin-NADP+ oxidoreductase from Bacillus subtilis (FORM II)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3LZWPDB ENTRY 3LZW

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP829320% PEG 3350, 0.2M Sodium fluoride, 5% Trehalose, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6854.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 207.466α = 90
b = 64.85β = 105.82
c = 61.116γ = 90
Symmetry
Space GroupC 1 2 1

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
11.926.8596.90.0513.659771
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)
1.91.9780.40.223

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 3LZW1.926.855672830141000.182670.181130.2111RANDOM26.974
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]
-1.37-0.99-0.311.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.38
r_dihedral_angle_4_deg15.436
r_dihedral_angle_3_deg12.673
r_dihedral_angle_1_deg5.608
r_scangle_it2.423
r_scbond_it1.505
r_angle_refined_deg1.325
r_mcangle_it0.965
r_angle_other_deg0.81
r_mcbond_it0.513
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.38
r_dihedral_angle_4_deg15.436
r_dihedral_angle_3_deg12.673
r_dihedral_angle_1_deg5.608
r_scangle_it2.423
r_scbond_it1.505
r_angle_refined_deg1.325
r_mcangle_it0.965
r_angle_other_deg0.81
r_mcbond_it0.513
r_symmetry_vdw_other0.219
r_nbd_refined0.189
r_symmetry_hbond_refined0.189
r_nbd_other0.182
r_nbtor_refined0.174
r_metal_ion_refined0.144
r_xyhbond_nbd_refined0.132
r_chiral_restr0.129
r_mcbond_other0.107
r_nbtor_other0.081
r_symmetry_vdw_refined0.067
r_bond_refined_d0.009
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 Atoms5140
Nucleic Acid Atoms
Solvent Atoms516
Heterogen Atoms204

Software

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