X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1K0M 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5293.150.02M Sodium potassium phosphate, 0.1M Bis-Tris propane pH 6.5, 20% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.2745.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.02α = 90
b = 70.655β = 90.13
c = 82.412γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2013-10-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
12.50382.41297.20.0620.0710.0350.99816.24.116309
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.5032.549940.4420.5090.2490.8974

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 REPLACEMENTTHROUGHOUT1K0M2.5142.061539679597.390.17810.17520.2356RANDOM43.751
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]
-3.690.585.46-1.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.98
r_dihedral_angle_3_deg18.444
r_dihedral_angle_4_deg16.331
r_dihedral_angle_1_deg6.29
r_angle_refined_deg1.602
r_angle_other_deg1.305
r_chiral_restr0.078
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.98
r_dihedral_angle_3_deg18.444
r_dihedral_angle_4_deg16.331
r_dihedral_angle_1_deg6.29
r_angle_refined_deg1.602
r_angle_other_deg1.305
r_chiral_restr0.078
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3640
Nucleic Acid Atoms
Solvent Atoms83
Heterogen Atoms

Software

Software
Software NamePurpose
XDSdata reduction
autoPROCdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHENIXphasing