6OT9

Bimetallic dodecameric cage design 1 (BMC1) from cytochrome cb562


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3M4B 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5298Protein solution: 2.1 mM protein, 1.05 mM Fe, 2 mM Zn added 1 hour prior to crystallisation. 1 ul + 1ul drops from protein solution and following mother liquor; 22.5% PEG400, 0.1 M HEPES pH 7.5, 0.2 M NaCl
Crystal Properties
Matthews coefficientSolvent content
2.652.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 125.64α = 90
b = 125.64β = 90
c = 166.35γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MMirror: Flat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M22018-04-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-20.98008SSRLBL12-2

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
12.439.9299.810.1850.1950.0610.9988.110.293824551.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.461002.9863.1460.5010.9610.072

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3M4B2.436.271.3438194374799.690.22280.21740.2718Random69.94
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
f_dihedral_angle_d9.1259
f_angle_d1.0358
f_chiral_restr0.0457
f_bond_d0.0088
f_plane_restr0.0049
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3268
Nucleic Acid Atoms
Solvent Atoms19
Heterogen Atoms200

Software

Software
Software NamePurpose
PHENIXrefinement
Blu-Icedata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing