Experiment: 3ZIY

 3ZIY

Structure of three-domain heme-Cu nitrite reductase from Ralstonia pickettii at 1.01 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2Z00PDB ENTRY 2Z00

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.5PEG, SODIUM CITRITE, pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.4850

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 128.177α = 90
b = 128.177β = 90
c = 86.314γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MMIRRORS2012-10-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 1SOLEILPROXIMA 1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.01401000.08184.32777286.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.011.0599.90.6223.4

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 2Z001.0137.762636991402999.910.109620.108980.12182RANDOM12.6
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]
-0.01-0.01-0.010.02
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free45.916
r_dihedral_angle_2_deg39.116
r_dihedral_angle_4_deg20.71
r_dihedral_angle_3_deg12.101
r_sphericity_bonded9.78
r_dihedral_angle_1_deg6.782
r_rigid_bond_restr4.678
r_angle_other_deg2.207
r_angle_refined_deg1.855
r_chiral_restr0.117
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3440
Nucleic Acid Atoms
Solvent Atoms794
Heterogen Atoms45

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing