3NPR

Crystal structure of the C(30) carotenoid dehydrosqualene synthase from S. aureus complexed with Presqualene diphosphate (PSPP)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ZCOPDB enry 2ZCO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.42980.2 M Potassium sodium tartrate tetrahydrate, 20% w/v Polyethylene glycol 3,350, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4750.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.571α = 90
b = 80.571β = 90
c = 91.672γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2010-04-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G1.0APS21-ID-G

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
123097.060.0664.1232282177822

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 enry 2ZCO2302322821778117697.060.201210.201210.197570.26846RANDOM39.206
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]
1.040.521.04-1.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.768
r_dihedral_angle_4_deg23.572
r_dihedral_angle_3_deg17.109
r_dihedral_angle_1_deg6.829
r_scangle_it6.183
r_scbond_it4.137
r_mcangle_it2.723
r_mcbond_it1.596
r_angle_refined_deg1.159
r_chiral_restr0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.768
r_dihedral_angle_4_deg23.572
r_dihedral_angle_3_deg17.109
r_dihedral_angle_1_deg6.829
r_scangle_it6.183
r_scbond_it4.137
r_mcangle_it2.723
r_mcbond_it1.596
r_angle_refined_deg1.159
r_chiral_restr0.09
r_gen_planes_refined0.015
r_bond_refined_d0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2392
Nucleic Acid Atoms
Solvent Atoms203
Heterogen Atoms41

Software

Software
Software NamePurpose
HKL-2000data collection
PHASESphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling