5IYS

Crystal structure of a dehydrosqualene synthase in complex with ligand


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4E9U 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529824% PEG 3350, 0.1M Li2SO4, 0.1M Bis-Tris pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.1141.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.238α = 90
b = 41.09β = 96.35
c = 93.477γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2015-11-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13C11.0NSRRCBL13C1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.9325980.0640.0760.0413.73.321148
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)
11.93297.10.2583.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4E9U1.932520009108897.450.16690.16410.2195RANDOM29.324
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]
0.24-0.66-0.850.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.417
r_dihedral_angle_4_deg20.969
r_dihedral_angle_3_deg15.951
r_scangle_it7.511
r_dihedral_angle_1_deg6.085
r_scbond_it4.894
r_mcangle_it2.801
r_mcbond_it1.76
r_angle_refined_deg1.445
r_chiral_restr0.111
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.417
r_dihedral_angle_4_deg20.969
r_dihedral_angle_3_deg15.951
r_scangle_it7.511
r_dihedral_angle_1_deg6.085
r_scbond_it4.894
r_mcangle_it2.801
r_mcbond_it1.76
r_angle_refined_deg1.445
r_chiral_restr0.111
r_gen_planes_refined0.017
r_bond_refined_d0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2325
Nucleic Acid Atoms
Solvent Atoms203
Heterogen Atoms61

Software

Software
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing