4PI0

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


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 dihydrate
Crystal Properties
Matthews coefficientSolvent content
3.3363.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.361α = 90
b = 184.739β = 90
c = 188.637γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMARMOSAIC 300 mm CCD2012-02-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D1.33765APS21-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
13.155077.821.513.755808

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 3RFR3.1550355808279678.210.22410.22110.2799RANDOM57.517
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]
-0.080.52-0.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.076
r_dihedral_angle_3_deg20.747
r_dihedral_angle_4_deg18.661
r_dihedral_angle_1_deg7.73
r_mcangle_it7.428
r_scbond_it4.781
r_mcbond_it4.536
r_angle_refined_deg1.683
r_chiral_restr0.12
r_bond_refined_d0.012
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.076
r_dihedral_angle_3_deg20.747
r_dihedral_angle_4_deg18.661
r_dihedral_angle_1_deg7.73
r_mcangle_it7.428
r_scbond_it4.781
r_mcbond_it4.536
r_angle_refined_deg1.683
r_chiral_restr0.12
r_bond_refined_d0.012
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms20624
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction