7CPM

CRYSTAL STRUCTURE OF DODECAPRENYL DIPHOSPHATE SYNTHASE FROM THERMOBIFIDA FUSCA


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP52980.1 M citric acid sodium citrate, 5% PEG6000
Crystal Properties
Matthews coefficientSolvent content
2.141.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.862α = 90
b = 137.59β = 90
c = 168.854γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702007-11-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A1Photon FactoryBL-17A

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
12.649.40999.80.05646.2017.352305
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)
12.62.691000.3715.1247.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1F752.649.40951548247999.8330.1910.1890.233663.085
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]
1.996-2.7480.752
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.606
r_dihedral_angle_4_deg17.774
r_dihedral_angle_3_deg15.467
r_lrange_other11.27
r_lrange_it11.267
r_scangle_it8.527
r_scangle_other8.525
r_mcangle_other7.88
r_mcangle_it7.879
r_dihedral_angle_1_deg5.902
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.606
r_dihedral_angle_4_deg17.774
r_dihedral_angle_3_deg15.467
r_lrange_other11.27
r_lrange_it11.267
r_scangle_it8.527
r_scangle_other8.525
r_mcangle_other7.88
r_mcangle_it7.879
r_dihedral_angle_1_deg5.902
r_scbond_it5.602
r_scbond_other5.602
r_mcbond_it5.471
r_mcbond_other5.468
r_angle_other_deg2.315
r_angle_refined_deg1.369
r_symmetry_xyhbond_nbd_refined0.248
r_symmetry_nbd_refined0.246
r_nbd_other0.222
r_symmetry_nbd_other0.22
r_nbd_refined0.2
r_nbtor_refined0.162
r_xyhbond_nbd_refined0.137
r_symmetry_nbtor_other0.077
r_chiral_restr0.06
r_bond_other_d0.035
r_gen_planes_other0.008
r_bond_refined_d0.007
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11544
Nucleic Acid Atoms
Solvent Atoms191
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing