X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52930.1 M Buffer system 3 (1 M Tris, 1 M BICINE, pH 8.5), 34-44% Precipitant Solution 3 (20% PEG 4000, 40%) and 60-80 mM Halogens Mix (NaF, NaBr and NaI) solution
Crystal Properties
Matthews coefficientSolvent content
2.0840.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.589α = 90
b = 42.962β = 90
c = 78.767γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.91188DiamondI04-1

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
11.0439.381000.0820.0890.0340.99911.312.362122
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)
11.041.066.2646.9643.020.4110.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5LRQ1.0439.3862033309599.9420.2120.2110.233318.865
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]
1.336-1.173-0.164
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it7.326
r_dihedral_angle_1_deg6.168
r_scangle_it4.944
r_dihedral_angle_2_deg3.805
r_scbond_it3.447
r_mcangle_it2.352
r_angle_refined_deg1.963
r_mcbond_it1.725
r_symmetry_nbd_refined0.375
r_nbtor_refined0.333
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it7.326
r_dihedral_angle_1_deg6.168
r_scangle_it4.944
r_dihedral_angle_2_deg3.805
r_scbond_it3.447
r_mcangle_it2.352
r_angle_refined_deg1.963
r_mcbond_it1.725
r_symmetry_nbd_refined0.375
r_nbtor_refined0.333
r_nbd_refined0.263
r_symmetry_xyhbond_nbd_refined0.248
r_xyhbond_nbd_refined0.166
r_chiral_restr0.11
r_gen_planes_refined0.014
r_bond_refined_d0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1076
Nucleic Acid Atoms
Solvent Atoms145
Heterogen Atoms17

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
Aimlessdata scaling
xia2data reduction
PHASERphasing