5L8D

X-ray structure of NikA from Escherichia coli in complex with Ru(bis(pyrzol-1-yl)acetate scorpionate)(CO)2Cl


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.72931.8 M ammonium sulfate, 100 mM sodium acetate pH 4.7
Crystal Properties
Matthews coefficientSolvent content
2.2445.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.303α = 90
b = 93.606β = 90
c = 124.211γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDADSC QUANTUM 315r2015-02-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30A0.979763ESRFBM30A

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
11.846.898.821.244.9892563

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 REPLACEMENTTHROUGHOUT3MVW1.846.887934462998.770.16970.16770.2082RANDOM27.073
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]
1.24-1.05-0.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.328
r_dihedral_angle_4_deg16.472
r_dihedral_angle_3_deg12.213
r_dihedral_angle_1_deg6.608
r_mcangle_it3.224
r_mcbond_it2.434
r_mcbond_other2.412
r_angle_other_deg2.347
r_angle_refined_deg1.898
r_chiral_restr0.119
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.328
r_dihedral_angle_4_deg16.472
r_dihedral_angle_3_deg12.213
r_dihedral_angle_1_deg6.608
r_mcangle_it3.224
r_mcbond_it2.434
r_mcbond_other2.412
r_angle_other_deg2.347
r_angle_refined_deg1.898
r_chiral_restr0.119
r_bond_refined_d0.02
r_gen_planes_other0.013
r_gen_planes_refined0.011
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7847
Nucleic Acid Atoms
Solvent Atoms666
Heterogen Atoms159

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing