5I6K

Crystal Structure of Copper Nitrite Reductase at 100K after 0.69 MGy


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BWI 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION4.52981.7 M Ammonium Sulphate, 0.1 M Sodium Acetate pH 4.5
Crystal Properties
Matthews coefficientSolvent content
1.9837.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.287α = 90
b = 95.287β = 90
c = 95.287γ = 90
Symmetry
Space GroupP 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2013-12-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.0742.6196.70.0480.0540.0260.99913.43.9121734
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.071.0987.90.8891.0750.5920.5412.75443

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 REPLACEMENTTHROUGHOUT2BWI1.0742.61115651606996.310.13960.13830.1623RANDOM14.026
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_deg35.206
r_sphericity_free29.044
r_dihedral_angle_4_deg19.196
r_dihedral_angle_3_deg12.332
r_sphericity_bonded8.242
r_dihedral_angle_1_deg8.164
r_rigid_bond_restr2.102
r_mcangle_it1.794
r_angle_refined_deg1.771
r_mcbond_it1.588
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.206
r_sphericity_free29.044
r_dihedral_angle_4_deg19.196
r_dihedral_angle_3_deg12.332
r_sphericity_bonded8.242
r_dihedral_angle_1_deg8.164
r_rigid_bond_restr2.102
r_mcangle_it1.794
r_angle_refined_deg1.771
r_mcbond_it1.588
r_mcbond_other1.576
r_angle_other_deg1.017
r_chiral_restr0.114
r_bond_refined_d0.014
r_gen_planes_refined0.009
r_bond_other_d0.003
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2581
Nucleic Acid Atoms
Solvent Atoms382
Heterogen Atoms23

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing