3POT

Structural analysis of a Ni(III)-methyl species in methyl-coenzyme M reductase from Methanothermobacter marburgensis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3M2RPDB ID: 3M2R, but with all waters, coenzymes and metal ions removed

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5294100 mM Hepes-Na pH 7.5, 150 mM magnesium acetate and 20% PEG 400., VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.1643.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.886α = 90
b = 118.165β = 91.94
c = 122.388γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80CCDADSC QUANTUM 315r2009-06-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.9794APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.2501000.07519.53.9721334721334-313.27
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.21.241000.433.73.772029

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 ID: 3M2R, but with all waters, coenzymes and metal ions removed1.2506858086851223612899.90.132950.131730.1562RANDOM12.192
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]
-0.03-0.150.39-0.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.544
r_dihedral_angle_4_deg16.926
r_dihedral_angle_3_deg12.331
r_dihedral_angle_1_deg6.295
r_scangle_it4.295
r_scbond_it2.677
r_angle_refined_deg1.93
r_mcangle_it1.761
r_rigid_bond_restr1.565
r_mcbond_it1.088
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.544
r_dihedral_angle_4_deg16.926
r_dihedral_angle_3_deg12.331
r_dihedral_angle_1_deg6.295
r_scangle_it4.295
r_scbond_it2.677
r_angle_refined_deg1.93
r_mcangle_it1.761
r_rigid_bond_restr1.565
r_mcbond_it1.088
r_chiral_restr0.128
r_bond_refined_d0.02
r_gen_planes_refined0.013
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms19098
Nucleic Acid Atoms
Solvent Atoms2602
Heterogen Atoms241

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing