2P8U

Crystal structure of human 3-hydroxy-3-methylglutaryl CoA synthase I


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52970.2M (NH4)2SO4, 0.1M Bis-Tris pH 6.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Crystal Properties
Matthews coefficientSolvent content
2.3748.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.762α = 90
b = 92.762β = 90
c = 235.532γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2006-12-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.99999SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
125094.40.12856666866668
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0799.70.7226.1

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 entries 2FA0,2F82,2FA3,2F9A,1XPL2506310863108338094.50.161490.161490.159330.20227RANDOM24.337
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]
0.220.22-0.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.212
r_dihedral_angle_4_deg17.088
r_dihedral_angle_3_deg12.14
r_scangle_it7.182
r_dihedral_angle_1_deg6.02
r_scbond_it5.87
r_mcangle_it3.463
r_mcbond_it2.52
r_angle_other_deg1.378
r_angle_refined_deg1.345
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.212
r_dihedral_angle_4_deg17.088
r_dihedral_angle_3_deg12.14
r_scangle_it7.182
r_dihedral_angle_1_deg6.02
r_scbond_it5.87
r_mcangle_it3.463
r_mcbond_it2.52
r_angle_other_deg1.378
r_angle_refined_deg1.345
r_mcbond_other0.654
r_symmetry_vdw_other0.227
r_nbd_refined0.205
r_nbd_other0.192
r_nbtor_refined0.177
r_symmetry_vdw_refined0.172
r_symmetry_hbond_refined0.154
r_xyhbond_nbd_refined0.142
r_nbtor_other0.093
r_chiral_restr0.082
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7135
Nucleic Acid Atoms
Solvent Atoms745
Heterogen Atoms102

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing