5VQ4

Nitrogenase Av1 at pH 5


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3U7Q 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293PEG 4000, sodium chloride, imidazole/malate, sodium dithionite
Crystal Properties
Matthews coefficientSolvent content
2.3146.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.315α = 90
b = 128.859β = 110.89
c = 108.359γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-03-10MSINGLE 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
12.339.5498.80.1749.26.791309
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)
12.32.3499.40.723.17.1

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 REPLACEMENTTHROUGHOUT3U7Q2.339.5486949432098.660.170310.16770.22242RANDOM24.883
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]
1.210.140.81-1.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.318
r_dihedral_angle_4_deg19.494
r_dihedral_angle_3_deg14.628
r_long_range_B_refined6.989
r_long_range_B_other6.875
r_dihedral_angle_1_deg6.087
r_scangle_other5.428
r_mcangle_it4.135
r_mcangle_other4.135
r_scbond_other3.712
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.318
r_dihedral_angle_4_deg19.494
r_dihedral_angle_3_deg14.628
r_long_range_B_refined6.989
r_long_range_B_other6.875
r_dihedral_angle_1_deg6.087
r_scangle_other5.428
r_mcangle_it4.135
r_mcangle_other4.135
r_scbond_other3.712
r_scbond_it3.711
r_mcbond_it2.933
r_mcbond_other2.932
r_angle_refined_deg1.39
r_angle_other_deg0.758
r_chiral_restr0.083
r_bond_refined_d0.011
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 Atoms15928
Nucleic Acid Atoms
Solvent Atoms362
Heterogen Atoms96

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata scaling
Aimlessdata scaling
PHASERphasing