6XBQ

Streptomyces coelicolor methylmalonyl-CoA epimerase in complex with carboxy-carba(dethia)-CoA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JC5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7298100 mM sodium chloride, 100 mM Bis-Tris:HCl pH 7.0, 2 M ammonium sulfate, 5% PEG 400
Crystal Properties
Matthews coefficientSolvent content
3.6966.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.504α = 90
b = 68.504β = 90
c = 103.315γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80IMAGE PLATEMAR scanner 300 mm plateMD2 microdiffractometer2018-10-25MSINGLE 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)CC (Half)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
11.64301000.1470.1390.1530.0411270.414.230657
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.641.711000.8860.8720.9190.2430.8747.714.2

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 REPLACEMENTTHROUGHOUT1JC51.6428.5629049154599.670.15550.15440.1752RANDOM28.474
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]
0.410.41-0.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.27
r_dihedral_angle_4_deg12.544
r_dihedral_angle_3_deg11.388
r_dihedral_angle_1_deg7.405
r_angle_refined_deg2.176
r_angle_other_deg1.622
r_chiral_restr0.304
r_bond_refined_d0.016
r_gen_planes_refined0.011
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.27
r_dihedral_angle_4_deg12.544
r_dihedral_angle_3_deg11.388
r_dihedral_angle_1_deg7.405
r_angle_refined_deg2.176
r_angle_other_deg1.622
r_chiral_restr0.304
r_bond_refined_d0.016
r_gen_planes_refined0.011
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1109
Nucleic Acid Atoms
Solvent Atoms199
Heterogen Atoms62

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
ARP/wARPmodel building
HKL-2000data reduction