X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5K7Y 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2930.1 M MOPS/HEPES-Na pH 7.5; 0.03 M of each divalent cation ; 10% w/v PEG 4000, 20% v/v glycerol A7 Morpheus condition
Crystal Properties
Matthews coefficientSolvent content
3.3863.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.612α = 90
b = 126.862β = 90
c = 130.572γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252016-03-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.30.894BESSY14.3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim 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
11.96948.4399.80.0990.1120.99813.64.65403230.67
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.972.0999.30.7510.8490.7031.984.58

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 REPLACEMENTTHROUGHOUT5K7Y248.4349530210099.850.17210.17080.2033RANDOM32.031
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]
0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.268
r_dihedral_angle_4_deg16.546
r_dihedral_angle_3_deg13.022
r_dihedral_angle_1_deg6.326
r_angle_other_deg3.583
r_angle_refined_deg1.512
r_chiral_restr0.091
r_bond_refined_d0.012
r_gen_planes_other0.011
r_gen_planes_refined0.007
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.268
r_dihedral_angle_4_deg16.546
r_dihedral_angle_3_deg13.022
r_dihedral_angle_1_deg6.326
r_angle_other_deg3.583
r_angle_refined_deg1.512
r_chiral_restr0.091
r_bond_refined_d0.012
r_gen_planes_other0.011
r_gen_planes_refined0.007
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3858
Nucleic Acid Atoms
Solvent Atoms467
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing
XDSdata reduction
Cootmodel building
XDSdata scaling