X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5N4C 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.2 M sodium acetate, 0.1 M Bis-Tris propane (pH 6.0-6.5) and 28% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.0840.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.01α = 115.81
b = 104.61β = 98.87
c = 110.65γ = 93.79
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-06-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9762DiamondI03

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
1255.84980.090.1080.996153.3182773
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)
122.0396.91.2341.460.54513.5

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 REPLACEMENTTHROUGHOUT5N4C255.84173300944597.930.2070.20530.238RANDOM45.089
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]
3.191.210.6-0.25-1.28-1.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.162
r_dihedral_angle_4_deg16.634
r_dihedral_angle_3_deg13.98
r_dihedral_angle_1_deg7.086
r_angle_refined_deg1.431
r_angle_other_deg1.216
r_chiral_restr0.064
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.162
r_dihedral_angle_4_deg16.634
r_dihedral_angle_3_deg13.98
r_dihedral_angle_1_deg7.086
r_angle_refined_deg1.431
r_angle_other_deg1.216
r_chiral_restr0.064
r_bond_refined_d0.007
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 Atoms23327
Nucleic Acid Atoms
Solvent Atoms682
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
APEXdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction