2F82

HMG-CoA synthase from Brassica juncea in the apo-form


X-RAY DIFFRACTION

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
2.3447.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.13α = 90
b = 61.13β = 90
c = 433.67γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42004-11-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.934ESRFID14-1

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
12.150980.07220.162958029353
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)
12.12.2289.50.3144.884188

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: 1TXT2.147.67293532796314721000.197240.197240.1950.23958RANDOM32.864
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]
0.090.050.09-0.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.537
r_dihedral_angle_4_deg22.128
r_dihedral_angle_3_deg18.246
r_dihedral_angle_1_deg6.557
r_scangle_it3.428
r_scbond_it2.39
r_angle_refined_deg1.546
r_mcangle_it1.497
r_mcbond_it0.925
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.537
r_dihedral_angle_4_deg22.128
r_dihedral_angle_3_deg18.246
r_dihedral_angle_1_deg6.557
r_scangle_it3.428
r_scbond_it2.39
r_angle_refined_deg1.546
r_mcangle_it1.497
r_mcbond_it0.925
r_nbtor_refined0.306
r_nbd_refined0.215
r_symmetry_vdw_refined0.182
r_xyhbond_nbd_refined0.155
r_symmetry_hbond_refined0.113
r_chiral_restr0.099
r_bond_refined_d0.015
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 Atoms3510
Nucleic Acid Atoms
Solvent Atoms153
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
NEMOdata reduction
XDSdata scaling
MOLREPphasing