5OGF | pdb_00005ogf

Cu nitrite reductase serial data at varying temperatures RT 0.27MGy


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5I6K 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5298100 mM sodium citrate at pH 5.0 and ~1.7 M ammonium sulphate
Crystal Properties
Matthews coefficientSolvent content
2.0439.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.263α = 90
b = 96.263β = 90
c = 96.263γ = 90
Symmetry
Space GroupP 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298PIXELPSI PILATUS 6M2015-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.8DiamondI24

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim I (All)CC (Half)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
11.8848.1399.50.1040.994.53.324354
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.881.9397.60.460.61.43.2

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 REPLACEMENTTHROUGHOUT5I6K1.8848.1323008120199.020.185040.183390.190.21590.22RANDOM21.971
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_deg37.582
r_dihedral_angle_4_deg18.225
r_dihedral_angle_3_deg13.432
r_dihedral_angle_1_deg7.486
r_long_range_B_refined5.295
r_long_range_B_other5.146
r_scangle_other3.132
r_mcangle_it2.173
r_mcangle_other2.173
r_scbond_it1.952
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2566
Nucleic Acid Atoms
Solvent Atoms124
Heterogen Atoms23

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata collection
XDSdata reduction
Aimlessdata scaling
REFMACphasing