5DQN

Polyethylene 600-bound form of P450 CYP125A3 mutant from Myobacterium Smegmatis - W83Y


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4APY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.2298Well contents (JCSG Core-III screen, G4): 0.1M Phosphate-Citrate buffer, pH 4.2 PEG 600, 40% v/v Drop Contents: 90% Well contents (see above) 10% Silver Bullets screen, B18: - 0.33% w/v 2,6-Naphthalenedisulfonic acid disodium salt - 0.33% w/v 2-Aminobenzenedisulfonic acid - 0.33% w/v m-Benzenedisulfonic acid disodium salt 0.02M HEPES sodium, pH 6.8
Crystal Properties
Matthews coefficientSolvent content
3.7467.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.821α = 90
b = 108.821β = 90
c = 118.809γ = 90
Symmetry
Space GroupI 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray98CCDADSC QUANTUM 3152015-07-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.11585ALS8.3.1

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
11.7680.32299.670.0427419.3723218551.5

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-VALUE4APY2.26280.2470.9532185309999.180.16680.16460.2088Random selection63.4
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_d13.049
f_angle_d0.799
f_chiral_restr0.03
f_bond_d0.004
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3206
Nucleic Acid Atoms
Solvent Atoms86
Heterogen Atoms82

Software

Software
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling