X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4U2M 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.62910.2 % PEG 4000, 0.1 M sodium citrate pH 5.6
Crystal Properties
Matthews coefficientSolvent content
3.2862.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.09α = 90
b = 115.19β = 90
c = 58.29γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2014-04-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97949DiamondI04

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
12.350.9399.70.0324433315
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)
12.32.3699.70.6632.44.2

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 REPLACEMENTTHROUGHOUT4U2M2.350.9333267165799.540.24020.23770.2863RANDOM64.693
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]
-2.071.570.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.932
r_dihedral_angle_4_deg22.959
r_dihedral_angle_3_deg15.406
r_mcangle_it8.224
r_mcbond_other6.347
r_mcbond_it6.345
r_dihedral_angle_1_deg5.776
r_angle_other_deg3.664
r_angle_refined_deg1.623
r_chiral_restr0.093
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.932
r_dihedral_angle_4_deg22.959
r_dihedral_angle_3_deg15.406
r_mcangle_it8.224
r_mcbond_other6.347
r_mcbond_it6.345
r_dihedral_angle_1_deg5.776
r_angle_other_deg3.664
r_angle_refined_deg1.623
r_chiral_restr0.093
r_bond_refined_d0.017
r_gen_planes_other0.014
r_gen_planes_refined0.008
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3562
Nucleic Acid Atoms
Solvent Atoms30
Heterogen Atoms

Software

Software
Software NamePurpose
XDSdata reduction
PDB_EXTRACTdata extraction
PHASERphasing
REFMACrefinement
Aimlessdata scaling
XSCALEdata reduction