X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherapo

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293Protein stock at 45 mg/mL in the buffer of 50 mM NaPO4 and 500 mM NaCl is mixed with the precipitant of 0.2 M KSCN, 21% PEG3350, 0.1 M bis-Tris propane pH 6.5, at a ratio of 1.2: 1.
Crystal Properties
Matthews coefficientSolvent content
2.551

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.2α = 90
b = 169.19β = 92.8
c = 169.69γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-09-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97951DiamondI04

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
11.9775.7799.80.07790.99811.64.1411803
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)
11.972.021000.9650.5581.44.2

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 REPLACEMENTTHROUGHOUTapo1.9775.774118032000699.750.1820.1810.2026RANDOM34.7035
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]
-0.120.19-1.031.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.813
r_dihedral_angle_4_deg18.044
r_dihedral_angle_3_deg14.038
r_dihedral_angle_1_deg6.399
r_angle_other_deg3.798
r_angle_refined_deg1.871
r_mcangle_it1.629
r_mcbond_it1.043
r_mcbond_other1.038
r_chiral_restr0.122
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.813
r_dihedral_angle_4_deg18.044
r_dihedral_angle_3_deg14.038
r_dihedral_angle_1_deg6.399
r_angle_other_deg3.798
r_angle_refined_deg1.871
r_mcangle_it1.629
r_mcbond_it1.043
r_mcbond_other1.038
r_chiral_restr0.122
r_bond_refined_d0.018
r_gen_planes_other0.017
r_gen_planes_refined0.01
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms41583
Nucleic Acid Atoms
Solvent Atoms2168
Heterogen Atoms368

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
xia2data reduction
xia2data scaling
Cootmodel building
MOLREPphasing