X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52930.2 M magnesium chloride, 0.1 M HEPES, 30% PEG400, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.2545.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.861α = 84.76
b = 45.628β = 83.22
c = 60.359γ = 78.6
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2014-02-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)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
11.659.7998.90.0890.050.99215.84.35386814.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6397.90.5110.2780.9294.64.32631

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 REPLACEMENTFREE R-VALUE3TIP1.659.7950959269498.470.20930.20710.249RANDOM25.569
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]
1.790.420.05-0.281.2-1.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.102
r_dihedral_angle_4_deg18.902
r_dihedral_angle_3_deg12.539
r_dihedral_angle_1_deg6.053
r_mcangle_it2.007
r_angle_refined_deg1.725
r_mcbond_other1.347
r_mcbond_it1.346
r_angle_other_deg1.115
r_chiral_restr0.101
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.102
r_dihedral_angle_4_deg18.902
r_dihedral_angle_3_deg12.539
r_dihedral_angle_1_deg6.053
r_mcangle_it2.007
r_angle_refined_deg1.725
r_mcbond_other1.347
r_mcbond_it1.346
r_angle_other_deg1.115
r_chiral_restr0.101
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.005
r_gen_planes_other0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3170
Nucleic Acid Atoms
Solvent Atoms257
Heterogen Atoms1

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing