8PXK

Structure of NADH-DEPENDENT FERREDOXIN REDUCTASE, BPHA4, solved at wavelength 5.76 A


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293Sodium formate Acetate buffer, pH 4.6
Crystal Properties
Matthews coefficientSolvent content
2.7455.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.186α = 90
b = 98.186β = 90
c = 170.292γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80PIXELDECTRIS PILATUS 12M2017-12-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I235.767DiamondI23

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
13.7785.0386.620.14480.15070.040150.99521.3811.94614
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.773.9050.987

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 DIFFRACTIONSADTHROUGHOUT3.7785.03438722886.730.185620.185350.19074RANDOM38.146
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]
-4.13-2.07-4.1313.41
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined20.552
r_long_range_B_other20.552
r_dihedral_angle_3_deg13.469
r_scangle_other11.647
r_scbond_it6.692
r_scbond_other6.21
r_dihedral_angle_1_deg6.205
r_dihedral_angle_2_deg4.375
r_mcangle_other4.035
r_mcangle_it4.031
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined20.552
r_long_range_B_other20.552
r_dihedral_angle_3_deg13.469
r_scangle_other11.647
r_scbond_it6.692
r_scbond_other6.21
r_dihedral_angle_1_deg6.205
r_dihedral_angle_2_deg4.375
r_mcangle_other4.035
r_mcangle_it4.031
r_mcbond_it2.398
r_mcbond_other2.393
r_angle_refined_deg1.431
r_angle_other_deg0.464
r_chiral_restr0.061
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3005
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms53

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
HKL2Mapphasing