X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4P3X4P3X (OPEN FORM) AND 5LQM (CLOSED FORM)
experimental modelPDB 5LQM4P3X (OPEN FORM) AND 5LQM (CLOSED FORM)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.8298PEG3350, TRIS, KCL, HEPES, PHTHALATE, Na2HPO4, ANAEROBIC
Crystal Properties
Matthews coefficientSolvent content
2.1342.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.14α = 103.82
b = 52.16β = 90.63
c = 58.95γ = 90.37
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2017-10-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.97242ESRFID23-1

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
1249.1390.20.0560.0720.0440.99612.12.434665
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)
122.0791.90.2760.3530.2170.8982.4

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 REPLACEMENTTHROUGHOUT4P3X (OPEN FORM) AND 5LQM (CLOSED FORM)243.4332832183190.220.19190.18960.2338RANDOM31.326
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]
-0.15-0.02-0.471.25-1.95-0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.156
r_dihedral_angle_4_deg19.375
r_dihedral_angle_3_deg14.301
r_dihedral_angle_1_deg5.253
r_angle_other_deg1.923
r_angle_refined_deg1.447
r_chiral_restr0.091
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_gen_planes_other0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.156
r_dihedral_angle_4_deg19.375
r_dihedral_angle_3_deg14.301
r_dihedral_angle_1_deg5.253
r_angle_other_deg1.923
r_angle_refined_deg1.447
r_chiral_restr0.091
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4811
Nucleic Acid Atoms
Solvent Atoms414
Heterogen Atoms40

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction