X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8CHOPDB ENTRY 8CHO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.22981.2 M ammonium sulfate, 20 mM potassium phosphate, 1 mM EDTA, 2 mM DTT, pH 7.2, vapor diffusion, sitting drop, temperature 298K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties
Matthews coefficientSolvent content
2.7755.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.041α = 90
b = 64.041β = 90
c = 502.22γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2010-02-06SINGLE WAVELENGTH
21x-ray100CCDMARMOSAIC 325 mm CCD2010-01-06SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-10.98SSRLBL9-1
2SYNCHROTRONSSRL BEAMLINE BL9-20.98SSRLBL9-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
1,2229.90999.60.16221.826.4432834328321.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1,222.1197.30.8124.721.45933

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 ENTRY 8CHO229.94297542975215999.580.1690.1690.1670.213RANDOM21.123
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]
1.170.591.17-1.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.288
r_dihedral_angle_4_deg20.605
r_dihedral_angle_3_deg13.819
r_dihedral_angle_1_deg6.247
r_scangle_it5.477
r_scbond_it3.541
r_angle_refined_deg1.96
r_mcangle_it1.944
r_mcbond_it1.159
r_chiral_restr0.154
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.288
r_dihedral_angle_4_deg20.605
r_dihedral_angle_3_deg13.819
r_dihedral_angle_1_deg6.247
r_scangle_it5.477
r_scbond_it3.541
r_angle_refined_deg1.96
r_mcangle_it1.944
r_mcbond_it1.159
r_chiral_restr0.154
r_bond_refined_d0.026
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3760
Nucleic Acid Atoms
Solvent Atoms398
Heterogen Atoms135

Software

Software
Software NamePurpose
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
XDSdata reduction