3UBR

Laue structure of Shewanella oneidensis cytochrome-c Nitrite Reductase


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.2529614% PEG 4K, pH 8.25, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal Properties
Matthews coefficientSolvent content
2.7955.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.5α = 90
b = 95.9β = 90
c = 223.8γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray273CCDMAR CCD 165 mm2011-06-17LLAUE
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-ID-B1.05-1.15APS14-ID-B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.591001000.0990.09916.77.72587525875
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.592.7240.57.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2RDZ2.5940.562245612456113151000.1950.1950.190240.28462RANDOM22.071
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]
0.03-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.973
r_dihedral_angle_3_deg21.008
r_dihedral_angle_4_deg15.893
r_dihedral_angle_1_deg8.062
r_scangle_it1.784
r_angle_refined_deg1.531
r_scbond_it1.095
r_angle_other_deg0.945
r_mcangle_it0.862
r_mcbond_it0.463
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.973
r_dihedral_angle_3_deg21.008
r_dihedral_angle_4_deg15.893
r_dihedral_angle_1_deg8.062
r_scangle_it1.784
r_angle_refined_deg1.531
r_scbond_it1.095
r_angle_other_deg0.945
r_mcangle_it0.862
r_mcbond_it0.463
r_chiral_restr0.081
r_mcbond_other0.067
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6946
Nucleic Acid Atoms
Solvent Atoms155
Heterogen Atoms432

Software

Software
Software NamePurpose
LaueCollectdata collection
PHASERphasing
REFMACrefinement
Precognitiondata reduction
Epinormdata reduction