X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7293Protein, at the concentration 15 mg/ml in 50 mM HEPES buffer pH 7 and 150 mM sodium chloride was mixed with equivolume solution of precipitant that contained, 17% (w/v) PEG3350 and 0.17 M ammonium citrate pH 7. Resulting droplets were equilibrated against the precipitant. For the data collection, crystal was briefly transferred to cryo-protecting solution, which had the same composition as precipitant, except concentration of PEG3350 was increased to 35 % (v/w/) and 10% (v/v), and also contained 15% of glycerol
Crystal Properties
Matthews coefficientSolvent content
2.1141.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 151.885α = 90
b = 62.509β = 118.19
c = 143.16γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER R 4MMultilayer X-ray mirrors VariMax HF2018-07-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.934096.10.10.1190.0647.83.386035
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)
11.931.96790.5120.6280.3590.6462.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT1.9326.5483055264995.950.15470.15240.2274RANDOM33.522
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]
0.090.04-0.40.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.891
r_dihedral_angle_4_deg18.538
r_dihedral_angle_3_deg15.285
r_dihedral_angle_1_deg7.386
r_angle_refined_deg2.317
r_angle_other_deg1.569
r_chiral_restr0.11
r_bond_refined_d0.02
r_gen_planes_refined0.015
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.891
r_dihedral_angle_4_deg18.538
r_dihedral_angle_3_deg15.285
r_dihedral_angle_1_deg7.386
r_angle_refined_deg2.317
r_angle_other_deg1.569
r_chiral_restr0.11
r_bond_refined_d0.02
r_gen_planes_refined0.015
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9410
Nucleic Acid Atoms
Solvent Atoms1184
Heterogen Atoms34

Software

Software
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
REFMACphasing