3M30

Structural Insight into Methyl-Coenzyme M Reductase Chemistry using Coenzyme B Analogues


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP282PEG 400, magnesium acetate, vapor diffusion, sitting drop, temperature 282K
Crystal Properties
Matthews coefficientSolvent content
2.1843.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.016α = 90
b = 118.26β = 91.84
c = 122.387γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-12-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-C0.90020APS14-BM-C

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
11.455098.10.05624.2833.540958740170113
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.451.595.40.4253.1673.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 SYNTHESISTHROUGHOUT1.4520.074137373814742016397.080.137270.135830.16438RANDOM13.931
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]
-0.07-0.090.66-0.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.466
r_dihedral_angle_4_deg16.969
r_dihedral_angle_3_deg13.42
r_dihedral_angle_1_deg6.374
r_scangle_it4.71
r_scbond_it2.949
r_angle_refined_deg2.549
r_mcangle_it1.909
r_mcbond_it1.276
r_chiral_restr0.197
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.466
r_dihedral_angle_4_deg16.969
r_dihedral_angle_3_deg13.42
r_dihedral_angle_1_deg6.374
r_scangle_it4.71
r_scbond_it2.949
r_angle_refined_deg2.549
r_mcangle_it1.909
r_mcbond_it1.276
r_chiral_restr0.197
r_bond_refined_d0.032
r_gen_planes_refined0.015
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms19098
Nucleic Acid Atoms
Solvent Atoms2368
Heterogen Atoms275

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
BioCARS-developeddata collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing