6XBR

Streptomyces coelicolor methylmalonyl-CoA epimerase (E43L) in complex with 2-nitronate-propionyl-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 Bis-Tris:HCl pH 7.0, 700 mM ammonium sulfate, 5% PEG 400
Crystal Properties
Matthews coefficientSolvent content
3.7166.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.601α = 90
b = 68.601β = 90
c = 103.582γ = 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 microdifractometer2019-04-05MSINGLE 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)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
11.553099.10.1040.1030.1080.0290.995437.913.83630126.597
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)
11.551.6198.20.8150.7220.8460.2270.8919.413.6

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 REPLACEMENTTHROUGHOUT1JC51.5529.4334540172098.880.15050.14950.1699RANDOM26.597
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]
-0.08-0.080.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.706
r_dihedral_angle_3_deg12.69
r_dihedral_angle_4_deg11.222
r_dihedral_angle_1_deg7.545
r_angle_refined_deg2.285
r_angle_other_deg1.874
r_chiral_restr0.256
r_bond_refined_d0.015
r_gen_planes_refined0.011
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.706
r_dihedral_angle_3_deg12.69
r_dihedral_angle_4_deg11.222
r_dihedral_angle_1_deg7.545
r_angle_refined_deg2.285
r_angle_other_deg1.874
r_chiral_restr0.256
r_bond_refined_d0.015
r_gen_planes_refined0.011
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1108
Nucleic Acid Atoms
Solvent Atoms268
Heterogen Atoms68

Software

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