5VPW

Nitrogenase Cp1 at pH 5


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4WES 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP298PEG 3350, magnesium chloride, Tris/HCl, sodium dithionite
Crystal Properties
Matthews coefficientSolvent content
2.6754

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.618α = 90
b = 146.282β = 103.55
c = 116.736γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-05-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-20.9795SSRLBL12-2

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
11.8539.298.40.07911.66.5189858
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)
11.851.8895.40.6822.56.2

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 REPLACEMENTTHROUGHOUT4WES1.8539.2180157963598.370.169070.167380.2007RANDOM28.823
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]
-1.070.381.8-0.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.743
r_dihedral_angle_4_deg21.302
r_dihedral_angle_3_deg14.726
r_long_range_B_other7.753
r_long_range_B_refined7.729
r_scangle_other6.628
r_dihedral_angle_1_deg5.993
r_scbond_it4.764
r_scbond_other4.764
r_mcangle_it4.641
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.743
r_dihedral_angle_4_deg21.302
r_dihedral_angle_3_deg14.726
r_long_range_B_other7.753
r_long_range_B_refined7.729
r_scangle_other6.628
r_dihedral_angle_1_deg5.993
r_scbond_it4.764
r_scbond_other4.764
r_mcangle_it4.641
r_mcangle_other4.64
r_mcbond_it3.594
r_mcbond_other3.594
r_angle_refined_deg1.411
r_angle_other_deg0.76
r_chiral_restr0.087
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms14928
Nucleic Acid Atoms
Solvent Atoms527
Heterogen Atoms96

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata scaling
Aimlessdata scaling
PHASERphasing
XDSdata reduction