8R8S | pdb_00008r8s

Low pH (5.5) as-isolated MSOX movie series dataset 1 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [0.57 MGy]


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6HBE 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52901.8 M ammonium sulfate with 50 mM Hepes buffer (pH 5.5)
Crystal Properties
Matthews coefficientSolvent content
2.5451.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.89α = 90
b = 103.89β = 90
c = 64.49γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2022-07-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.85504DiamondI24

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.1152.42990.0690.0350.9988.94.215426810.94
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.111.1398.61.5150.8430.340.83.7

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.1152146576765998.970.118270.117050.120.141390.14RANDOM16.495
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]
-0.31-0.15-0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.071
r_dihedral_angle_4_deg18.56
r_dihedral_angle_3_deg12.402
r_dihedral_angle_1_deg7.99
r_rigid_bond_restr4.096
r_long_range_B_refined3.65
r_scbond_it3.477
r_long_range_B_other2.957
r_scangle_other2.891
r_scbond_other2.762
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.071
r_dihedral_angle_4_deg18.56
r_dihedral_angle_3_deg12.402
r_dihedral_angle_1_deg7.99
r_rigid_bond_restr4.096
r_long_range_B_refined3.65
r_scbond_it3.477
r_long_range_B_other2.957
r_scangle_other2.891
r_scbond_other2.762
r_angle_refined_deg2.066
r_mcangle_other1.795
r_mcangle_it1.782
r_mcbond_it1.764
r_mcbond_other1.714
r_angle_other_deg1.522
r_chiral_restr0.129
r_bond_refined_d0.018
r_gen_planes_refined0.013
r_gen_planes_other0.003
r_bond_other_d0.001
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_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2553
Nucleic Acid Atoms
Solvent Atoms527
Heterogen Atoms45

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
MOLREPphasing