X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YWTPDB ENTRY 1YWT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52770.1M HEPES, 0.2M calcium chloride, 28% PEG 400, 5% glycerol, 2mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.4750.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.32α = 90
b = 112.32β = 90
c = 62.66γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2009-02-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.85SLSX10SA

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
11.2845.5799.20.08820.810.674319-3-318.258
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)
1.281.398.20.5795.19.23304

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)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 1YWT1.2845.57-3-3743197060337161000.1280.1280.1260.151RANDOM18.45
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]
0.130.25-0.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.603
r_dihedral_angle_4_deg16.98
r_dihedral_angle_3_deg12.895
r_dihedral_angle_1_deg11.817
r_scangle_it7.593
r_scbond_it5.233
r_mcangle_it3.621
r_rigid_bond_restr2.816
r_mcbond_it2.433
r_angle_refined_deg2.029
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.603
r_dihedral_angle_4_deg16.98
r_dihedral_angle_3_deg12.895
r_dihedral_angle_1_deg11.817
r_scangle_it7.593
r_scbond_it5.233
r_mcangle_it3.621
r_rigid_bond_restr2.816
r_mcbond_it2.433
r_angle_refined_deg2.029
r_chiral_restr0.117
r_bond_refined_d0.021
r_gen_planes_refined0.013
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1901
Nucleic Acid Atoms
Solvent Atoms404
Heterogen Atoms10

Software

Software
Software NamePurpose
ProDCdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling