X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3P53 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29216-20% PEG 3350, 200 mM LiAc, 4% glycerol
Crystal Properties
Matthews coefficientSolvent content
2.2545.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 159.91α = 90
b = 71.62β = 130.9
c = 113.32γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152012-07-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I041.0781DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.7736.7299.50.0450.0650.034163.79387223.131
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.771.8299.90.5350.7090.3652.33.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3P531.7736.7289166470599.450.19650.19490.2268RANDOM39.067
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]
-0.11.74-5.020.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.374
r_dihedral_angle_4_deg17.093
r_dihedral_angle_3_deg13.709
r_dihedral_angle_1_deg5.111
r_angle_refined_deg1.613
r_angle_other_deg1.601
r_mcangle_it1.086
r_mcbond_it0.665
r_mcbond_other0.665
r_chiral_restr0.099
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.374
r_dihedral_angle_4_deg17.093
r_dihedral_angle_3_deg13.709
r_dihedral_angle_1_deg5.111
r_angle_refined_deg1.613
r_angle_other_deg1.601
r_mcangle_it1.086
r_mcbond_it0.665
r_mcbond_other0.665
r_chiral_restr0.099
r_bond_refined_d0.014
r_gen_planes_other0.011
r_gen_planes_refined0.009
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7555
Nucleic Acid Atoms
Solvent Atoms587
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
xia2data scaling
PDB_EXTRACTdata extraction
xia2data reduction