3MVZ

X-ray structure of the (hydro)peroxo intermediate NikA/1-Int", after monohydroxylation of the iron complex


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.72931.8M ammonium acetate, 0.1M sodium acetate, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2645.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.727α = 90
b = 94.298β = 90
c = 124.557γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDADSC QUANTUM 2102009-04-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.9334ESRFID14-1

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
11.747.2930.06311.22.710594324.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.7930.2933.42.529711

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 1ZLQ1.747.1510594355761000.165810.163980.2004RANDOM17.236
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]
-0.2-0.50.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.683
r_dihedral_angle_4_deg15.29
r_dihedral_angle_3_deg13.423
r_dihedral_angle_1_deg6.096
r_scangle_it3.446
r_scbond_it2.132
r_angle_refined_deg1.391
r_mcangle_it1.361
r_mcbond_it0.846
r_chiral_restr0.105
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.683
r_dihedral_angle_4_deg15.29
r_dihedral_angle_3_deg13.423
r_dihedral_angle_1_deg6.096
r_scangle_it3.446
r_scbond_it2.132
r_angle_refined_deg1.391
r_mcangle_it1.361
r_mcbond_it0.846
r_chiral_restr0.105
r_bond_refined_d0.012
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7884
Nucleic Acid Atoms
Solvent Atoms1089
Heterogen Atoms193

Software

Software
Software NamePurpose
MxCuBEdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling