2F9A

HMG-CoA synthase from Brassica juncea in complex with F-244


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
2.2344.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.17α = 90
b = 61.17β = 90
c = 412.59γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42005-04-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30A0.979754ESRFBM30A

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
12.55096.80.119.9311.616476
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)
12.52.6583.40.44.89

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: 2F822.5150157461574683997.560.158050.158050.154040.23644RANDOM23.914
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]
0.110.060.11-0.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.499
r_dihedral_angle_4_deg22.263
r_dihedral_angle_3_deg19.157
r_dihedral_angle_1_deg6.982
r_scangle_it3.394
r_scbond_it2.191
r_angle_refined_deg1.706
r_mcangle_it1.444
r_mcbond_it0.838
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.499
r_dihedral_angle_4_deg22.263
r_dihedral_angle_3_deg19.157
r_dihedral_angle_1_deg6.982
r_scangle_it3.394
r_scbond_it2.191
r_angle_refined_deg1.706
r_mcangle_it1.444
r_mcbond_it0.838
r_nbtor_refined0.308
r_nbd_refined0.252
r_symmetry_vdw_refined0.199
r_xyhbond_nbd_refined0.171
r_symmetry_hbond_refined0.152
r_chiral_restr0.117
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3139
Nucleic Acid Atoms
Solvent Atoms273
Heterogen Atoms23

Software

Software
Software NamePurpose
REFMACrefinement
NEMOdata reduction
XDSdata scaling
MOLREPphasing