3QIM

Histidine 416 of the periplamsic binding protein NikA is essential for nickel uptake in Escherichia coli


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.72931.6M Ammonium sulfate, 100 mM sodium acetate, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2545.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.731α = 90
b = 94.005β = 90
c = 124.33γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2010-06-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM160.984ESRFBM16

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
12.124.84930.0612.932.656622227.4

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1ZLQ2.124.845662229811000.179110.176070.2369RANDOM27.411
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]
0.18-1.491.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.925
r_dihedral_angle_3_deg16.186
r_dihedral_angle_4_deg16.031
r_dihedral_angle_1_deg6.408
r_scangle_it3.946
r_scbond_it2.501
r_angle_refined_deg1.541
r_mcangle_it1.518
r_mcbond_it0.822
r_chiral_restr0.103
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.925
r_dihedral_angle_3_deg16.186
r_dihedral_angle_4_deg16.031
r_dihedral_angle_1_deg6.408
r_scangle_it3.946
r_scbond_it2.501
r_angle_refined_deg1.541
r_mcangle_it1.518
r_mcbond_it0.822
r_chiral_restr0.103
r_bond_refined_d0.015
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7897
Nucleic Acid Atoms
Solvent Atoms506
Heterogen Atoms120

Software

Software
Software NamePurpose
MXdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling