6Z4T

sperm whale myoglobin mutant (H64V V64A) bearing the non-canonical amino acid 2-Amino-3-(thiazol-5-yl)propanoic acid as axial heme ligand


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6G5T 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.1 M SPG 28-32% PEG 1500 180 nL protein 10mg/mL + 20 nL seed 100 nL well solution
Crystal Properties
Matthews coefficientSolvent content
2.1141.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.009α = 90
b = 47.327β = 90
c = 76.897γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M-F2020-01-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.000023SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.235094.20.99912.223.0977274
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.231.30.382

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-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6G5T1.2340.311.3477195382894.230.15190.150.187520.99
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_d19.0408
f_angle_d0.8847
f_chiral_restr0.0639
f_bond_d0.0056
f_plane_restr0.0041
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1215
Nucleic Acid Atoms
Solvent Atoms193
Heterogen Atoms45

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHENIXmodel building
PHENIXphasing
PHENIXrefinement