6XBV

Streptomyces coelicolor methylmalonyl-CoA epimerase (S115T) 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, and 5% PEG400
Crystal Properties
Matthews coefficientSolvent content
3.7967.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.309α = 90
b = 69.309β = 90
c = 103.562γ = 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
11.53099.90.1120.1010.1160.0310.994492.413.94125227.733
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)
11.51.5599.91.0920.9671.1340.3010.84713.8

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 REPLACEMENTTHROUGHOUT1JC51.526.6139173201299.780.15440.15310.1791RANDOM27.733
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]
0.030.03-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.923
r_dihedral_angle_4_deg12.977
r_dihedral_angle_3_deg12.855
r_dihedral_angle_1_deg7.495
r_angle_refined_deg2.375
r_angle_other_deg1.911
r_chiral_restr0.273
r_bond_refined_d0.017
r_gen_planes_refined0.012
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.923
r_dihedral_angle_4_deg12.977
r_dihedral_angle_3_deg12.855
r_dihedral_angle_1_deg7.495
r_angle_refined_deg2.375
r_angle_other_deg1.911
r_chiral_restr0.273
r_bond_refined_d0.017
r_gen_planes_refined0.012
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1110
Nucleic Acid Atoms
Solvent Atoms275
Heterogen Atoms67

Software

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