5MWU

Crystal structure of the periplasmic nickel-binding protein NikA from Escherichia coli in complex with Ru(bpza)(CO)2Cl


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.729315 mg/ml protei solution mixed with 1.8 M ammonium sulfate, 100 mM sodium acetate pH 4.7
Crystal Properties
Matthews coefficientSolvent content
2.2344.73

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 BM30A0.979769ESRFBM30A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.846.898.80.05721.244.989256327.6

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 REPLACEMENTTHROUGHOUT1ZLQ1.846.887934462998.770.169720.167690.20818RANDOM27.073
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_long_range_B_other6.229
r_long_range_B_refined6.228
r_scangle_other4.812
r_scbond_it3.317
r_scbond_other3.317
r_mcangle_it3.224
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_long_range_B_other6.229
r_long_range_B_refined6.228
r_scangle_other4.812
r_scbond_it3.317
r_scbond_other3.317
r_mcangle_it3.224
r_mcangle_other3.224
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
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 Atoms7847
Nucleic Acid Atoms
Solvent Atoms666
Heterogen Atoms159

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing