2FA3

HMG-CoA synthase from Brassica juncea in complex with acetyl-CoA and acetyl-cys117.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2F82PDB Entry: 2F82

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.527717% PEG 20K, 0.25M TMAO, 100mM PIPES, 2mM dithiothreitol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.2545.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.6α = 90
b = 61.6β = 90
c = 411.79γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2005-04-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30A0.978565ESRFBM30A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)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
12.55097.40.11316.267.916567
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.6685.60.4893.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB Entry: 2F822.5250158761587684898.30.181350.181350.176120.28168RANDOM28.532
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]
0.610.310.61-0.92
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.269
r_dihedral_angle_4_deg22.982
r_dihedral_angle_3_deg20.458
r_dihedral_angle_1_deg7.769
r_scangle_it3.722
r_scbond_it2.501
r_angle_refined_deg2.002
r_mcangle_it1.527
r_mcbond_it0.899
r_nbtor_refined0.317
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.269
r_dihedral_angle_4_deg22.982
r_dihedral_angle_3_deg20.458
r_dihedral_angle_1_deg7.769
r_scangle_it3.722
r_scbond_it2.501
r_angle_refined_deg2.002
r_mcangle_it1.527
r_mcbond_it0.899
r_nbtor_refined0.317
r_nbd_refined0.258
r_symmetry_vdw_refined0.223
r_xyhbond_nbd_refined0.187
r_symmetry_hbond_refined0.173
r_chiral_restr0.12
r_bond_refined_d0.021
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3513
Nucleic Acid Atoms
Solvent Atoms133
Heterogen Atoms51

Software

Software
Software NamePurpose
REFMACrefinement
NEMOdata reduction
XDSdata scaling
MOLREPphasing