6R4Q

Crystal structure of the periplasmic nickel-binding protein NikA from Escherichia coli in complex with Ru(bpza)CO H2O Cl


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ZLQ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.62930.1M Na acetate pH 4.6 1.8 M ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.2545.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.629α = 90
b = 94.101β = 90
c = 124.418γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDADSC QUANTUM 315r2015-02-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30A0.979758ESRFBM30A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.944.5299.916.067564360
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.92

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 REPLACEMENTTHROUGHOUT1ZLQ1.944.5276571403199.860.180360.177680.23191RANDOM24.17
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]
0.3-0.840.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.045
r_dihedral_angle_4_deg15.529
r_dihedral_angle_3_deg13.228
r_dihedral_angle_1_deg7.057
r_long_range_B_refined6.267
r_long_range_B_other6.267
r_scangle_other3.946
r_mcangle_other2.769
r_mcangle_it2.768
r_scbond_it2.599
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.045
r_dihedral_angle_4_deg15.529
r_dihedral_angle_3_deg13.228
r_dihedral_angle_1_deg7.057
r_long_range_B_refined6.267
r_long_range_B_other6.267
r_scangle_other3.946
r_mcangle_other2.769
r_mcangle_it2.768
r_scbond_it2.599
r_scbond_other2.599
r_mcbond_it1.915
r_mcbond_other1.893
r_angle_refined_deg1.56
r_angle_other_deg1.329
r_chiral_restr0.073
r_bond_refined_d0.009
r_gen_planes_refined0.008
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 Atoms7864
Nucleic Acid Atoms
Solvent Atoms738
Heterogen Atoms186

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing