3Q6J

Structural basis for carbon dioxide binding by 2-ketopropyl coenzyme M Oxidoreductase/Carboxylase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MO9PDB ENTRY 1MO9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.52940.17 M SODIUM ACETATE, 0.085 M TRIS-HCL, 25.5% PEG4000, 15% GLYCEROL, VAPOR DIFFUSION, HANGING DROP, temperature 294K, pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.3748.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.466α = 90
b = 59.803β = 102.28
c = 105.463γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-1SSRLBL9-1

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
11.882095.10.0935.583625
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.881.93

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 1MO91.92878689394296.70.1670.1640.221RANDOM24.26
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]
-0.010.010.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.284
r_dihedral_angle_4_deg15.081
r_dihedral_angle_3_deg13.619
r_scangle_it6.976
r_dihedral_angle_1_deg6.216
r_scbond_it5.288
r_mcangle_it4.955
r_mcbond_it4.159
r_angle_refined_deg1.453
r_chiral_restr0.094
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.284
r_dihedral_angle_4_deg15.081
r_dihedral_angle_3_deg13.619
r_scangle_it6.976
r_dihedral_angle_1_deg6.216
r_scbond_it5.288
r_mcangle_it4.955
r_mcbond_it4.159
r_angle_refined_deg1.453
r_chiral_restr0.094
r_bond_refined_d0.014
r_gen_planes_refined0.007
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 Atoms8044
Nucleic Acid Atoms
Solvent Atoms1062
Heterogen Atoms237

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing