X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YQWpdb entry 1YQW

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION8.5298PEG4000, LiSO4, DTT, DMM, pH 8.5, vapor diffusion, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0740.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.93α = 90
b = 97.79β = 90
c = 183.29γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rToroidal mirror2011-07-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.94645ESRFID23-1

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
11.6710098.30.06211.781.905372270194962-318.782
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)
11.671.7498.90.382.46

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 1YQW1.6729.82194961194961964499.770.12220.12220.11980.1684RANDOM13.1137
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]
0.050.33-0.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.327
r_dihedral_angle_4_deg16.695
r_dihedral_angle_3_deg12.445
r_scangle_it6.107
r_dihedral_angle_1_deg5.642
r_scbond_it4.386
r_mcangle_it2.928
r_rigid_bond_restr2.428
r_mcbond_it2.009
r_angle_refined_deg1.239
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.327
r_dihedral_angle_4_deg16.695
r_dihedral_angle_3_deg12.445
r_scangle_it6.107
r_dihedral_angle_1_deg5.642
r_scbond_it4.386
r_mcangle_it2.928
r_rigid_bond_restr2.428
r_mcbond_it2.009
r_angle_refined_deg1.239
r_chiral_restr0.086
r_bond_refined_d0.011
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13228
Nucleic Acid Atoms
Solvent Atoms1257
Heterogen Atoms151

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MxCuBEdata collection
XDSdata reduction