2Y1A | pdb_00002y1a

Crystal structure of Achromobacter cycloclastes Cu nitrite reductase with bound NO


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BW4PDB ENTRY 2BW4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.751.6M AMMONIUM SULPHATE, 100MM SODIUM ACETATE PH 4.75
Crystal Properties
Matthews coefficientSolvent content
236.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.24α = 90
b = 95.24β = 90
c = 95.24γ = 90
Symmetry
Space GroupP 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORSMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX10.1SRSPX10.1

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
11.9526.493.20.0419.64.4198070.1
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)
11.952.0258.40.086.71.8

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2BW41.9526.411814298989.980.156350.153410.160.209510.21RANDOM15.991
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.92
r_dihedral_angle_4_deg18.532
r_dihedral_angle_3_deg12.96
r_dihedral_angle_1_deg7.556
r_scangle_it2.686
r_scbond_it1.789
r_angle_refined_deg1.502
r_mcangle_it1.126
r_mcbond_it0.692
r_angle_other_deg0.683
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2565
Nucleic Acid Atoms
Solvent Atoms234
Heterogen Atoms32

Software

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