6N96

Methylmalonyl-CoA decarboxylase in complex with 2-sulfonate-propionyl-oxa(dethia)-CoA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1EF8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8298100 mM sodium chloride, 100 mM imidazole, 0.4 M Monosodium phosphate/1.6 M Dipotassium phosphate, 2% PEG 400
Crystal Properties
Matthews coefficientSolvent content
2.7655.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.148α = 90
b = 114.66β = 90
c = 192.705γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2017-04-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D0.97849APS21-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
11.73090.80.0990.1050.1080.0429.76.1191624-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7690.70.840.842.1165.7

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 REPLACEMENTTHROUGHOUT1EF81.729.96177529928188.160.15250.15090.1839RANDOM15.736
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]
-0.10.010.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.659
r_dihedral_angle_4_deg15.938
r_dihedral_angle_3_deg13.422
r_dihedral_angle_1_deg6.134
r_mcangle_it2.296
r_angle_refined_deg2.009
r_mcbond_it1.495
r_mcbond_other1.495
r_angle_other_deg1.483
r_chiral_restr0.161
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.659
r_dihedral_angle_4_deg15.938
r_dihedral_angle_3_deg13.422
r_dihedral_angle_1_deg6.134
r_mcangle_it2.296
r_angle_refined_deg2.009
r_mcbond_it1.495
r_mcbond_other1.495
r_angle_other_deg1.483
r_chiral_restr0.161
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12246
Nucleic Acid Atoms
Solvent Atoms1882
Heterogen Atoms739

Software

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