6N97

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8298150 mM sodium chloride, 100 mM imidazole, 0.4 M Monosodium phosphate/1.6 M Dipotassium phosphate
Crystal Properties
Matthews coefficientSolvent content
2.7555.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.961α = 90
b = 114.614β = 90
c = 192.338γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2018-10-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

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
11.753097.50.0930.0930.1010.0387.66.61242089189024-3
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)
1.751.8194.91.0181.0182.3876.5

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 REPLACEMENTTHROUGHOUT1EF81.7530179523937896.970.14910.14750.1794RANDOM24.896
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]
-0.74-1.532.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.717
r_dihedral_angle_4_deg17.289
r_dihedral_angle_3_deg14.554
r_dihedral_angle_1_deg6.3
r_mcangle_it2.858
r_mcbond_other2.039
r_mcbond_it2.038
r_angle_refined_deg2
r_angle_other_deg1.466
r_chiral_restr0.161
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.717
r_dihedral_angle_4_deg17.289
r_dihedral_angle_3_deg14.554
r_dihedral_angle_1_deg6.3
r_mcangle_it2.858
r_mcbond_other2.039
r_mcbond_it2.038
r_angle_refined_deg2
r_angle_other_deg1.466
r_chiral_restr0.161
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12246
Nucleic Acid Atoms
Solvent Atoms1912
Heterogen Atoms772

Software

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