X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3NMLPDB ENTRY 3NML

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1SMALL TUBES9293Solution of MB (carbonmonoxy-form) (20mg/ml protein in 0.02M TRIS-HCl pH 9.0) mixed with mother liquor (3.2M ammonium sulphate, 0.05M TRIS-HCl, pH 9.0) for final concentrations of 2.5M ammonium sulphate to obtain crystals of MBCO. MBCO crystals were oxidyzed by excess of potassium ferricyanide, washed in mother liquor and reduced under anaerobic conditions with sodium dithionite, SMALL TUBES, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3447.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.83α = 90
b = 47.13β = 90
c = 88.93γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2010-07-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R1.5418

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
11.623.5796.60.04315.53.6521466
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)
1.61.66910.2634.13.66

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 3NML1.623.56521429105596.380.18090.17980.2026RANDOM20.7404
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]
0.9137-0.4889-0.4248
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.507
f_angle_d1.088
f_chiral_restr0.07
f_bond_d0.006
f_plane_restr0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1229
Nucleic Acid Atoms
Solvent Atoms249
Heterogen Atoms88

Software

Software
Software NamePurpose
d*TREKdata processing
PHENIXrefinement
PDB_EXTRACTdata extraction
StructureStudiodata collection
d*TREKdata reduction
d*TREKdata scaling
CNSphasing