Experiment: 2P8U

 2P8U

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2FA0PDB entries 2FA0,2F82,2FA3,2F9A,1XPL
experimental modelPDB 2F82PDB entries 2FA0,2F82,2FA3,2F9A,1XPL
experimental modelPDB 2FA3PDB entries 2FA0,2F82,2FA3,2F9A,1XPL
experimental modelPDB 2F9APDB entries 2FA0,2F82,2FA3,2F9A,1XPL
experimental modelPDB 1XPLPDB entries 2FA0,2F82,2FA3,2F9A,1XPL

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
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