4PHZ

Crystal structure of particulate methane monooxygenase from Methylocystis sp. ATCC 49242 (Rockwell)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3RFRPDB entry 3RFR

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529510% PEG3000, 0.1 M sodium cacodylate trihydrate, pH 6.5, 0.2 M magnesium formate
Crystal Properties
Matthews coefficientSolvent content
358.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 117.462α = 90
b = 184.531β = 90
c = 189.417γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMARMOSAIC 300 mm CCD2011-10-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.37765APS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.595072.618.914.493278

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 REPLACEMENTTHROUGHOUTPDB entry 3RFR2.5950393278467872.320.23930.23670.2887RANDOM42.225
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]
-0.30.92-0.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.004
r_dihedral_angle_4_deg19.198
r_dihedral_angle_3_deg19.147
r_dihedral_angle_1_deg7.631
r_angle_refined_deg1.666
r_chiral_restr0.11
r_bond_refined_d0.012
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms20526
Nucleic Acid Atoms
Solvent Atoms117
Heterogen Atoms211

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction