6XBT

Streptomyces coelicolor methylmalonyl-CoA epimerase (Q60A) 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 DROP7298150 mM sodium chloride, 100 mM Bis-Tris:HCl pH 7.0, 2.3 M ammonium sulfate, and 5% PEG400
Crystal Properties
Matthews coefficientSolvent content
3.7367.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.774α = 90
b = 68.774β = 90
c = 103.617γ = 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
11.49301000.10.0910.1040.0280.985446.2144089427.36
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)
11.491.551000.8460.7080.8780.2340.9058.613.9

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 REPLACEMENTTHROUGHOUT1JC51.4929.538778204999.410.17080.17010.1841RANDOM27.36
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]
0.670.67-1.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.793
r_dihedral_angle_4_deg16.318
r_dihedral_angle_3_deg12.426
r_dihedral_angle_1_deg7.139
r_angle_refined_deg2.394
r_angle_other_deg1.812
r_chiral_restr0.181
r_bond_refined_d0.017
r_gen_planes_refined0.013
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.793
r_dihedral_angle_4_deg16.318
r_dihedral_angle_3_deg12.426
r_dihedral_angle_1_deg7.139
r_angle_refined_deg2.394
r_angle_other_deg1.812
r_chiral_restr0.181
r_bond_refined_d0.017
r_gen_planes_refined0.013
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1076
Nucleic Acid Atoms
Solvent Atoms233
Heterogen Atoms114

Software

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