X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3WU2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH62855% PEG 1450, 20MM NACL, 10MM CACL2, 40MM MGSO4, 20MM MES BUFFER, PH 6.0, MICRO-BATCH METHOD UNDER OIL, TEMPERATURE 285K
Crystal Properties
Matthews coefficientSolvent content
3.261.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.25α = 90
b = 228.43β = 90
c = 287.12γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2016-04-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.0SPring-8BL41XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.119.9999.50.0870.99813.76.8459862
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.2298.50.8860.872.16.7

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 REPLACEMENTTHROUGHOUT3WU22.119.994385022304399.310.15620.15410.1966RANDOM47.34
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]
0.01-0.020.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.053
r_dihedral_angle_4_deg17.601
r_dihedral_angle_3_deg13.574
r_dihedral_angle_1_deg6.115
r_angle_refined_deg2.582
r_angle_other_deg1.315
r_chiral_restr0.12
r_bond_refined_d0.021
r_gen_planes_refined0.013
r_gen_planes_other0.009
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.053
r_dihedral_angle_4_deg17.601
r_dihedral_angle_3_deg13.574
r_dihedral_angle_1_deg6.115
r_angle_refined_deg2.582
r_angle_other_deg1.315
r_chiral_restr0.12
r_bond_refined_d0.021
r_gen_planes_refined0.013
r_gen_planes_other0.009
r_bond_other_d0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms40940
Nucleic Acid Atoms
Solvent Atoms2356
Heterogen Atoms10055

Software

Software
Software NamePurpose
REFMACrefinement
Cootmodel building
PDB_EXTRACTdata extraction
MOLREPphasing
XDSdata reduction