6N94

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6N92 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829850 mM sodium chloride, 100 mM imidazole, 0.4 M Monosodium phosphate/1.6 M Dipotassium phosphate, 2% PEG 400
Crystal Properties
Matthews coefficientSolvent content
2.7755.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.046α = 90
b = 114.816β = 90
c = 193.732γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2016-08-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

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
11.75301000.1250.1250.1350.055.27.31422149194971-3
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)
11.751.781001.4891.4891.3127.3

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 REPLACEMENTTHROUGHOUT6N921.7529.29175192916494.030.14730.14570.1777RANDOM21.86
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]
-0.32-0.150.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.653
r_dihedral_angle_4_deg16.145
r_dihedral_angle_3_deg14.169
r_dihedral_angle_1_deg6.36
r_mcangle_it2.719
r_angle_refined_deg1.868
r_mcbond_other1.851
r_mcbond_it1.85
r_angle_other_deg1.509
r_chiral_restr0.116
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.653
r_dihedral_angle_4_deg16.145
r_dihedral_angle_3_deg14.169
r_dihedral_angle_1_deg6.36
r_mcangle_it2.719
r_angle_refined_deg1.868
r_mcbond_other1.851
r_mcbond_it1.85
r_angle_other_deg1.509
r_chiral_restr0.116
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 Atoms1893
Heterogen Atoms550

Software

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