X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5LB5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52930.2M sodium chloride -- 25% PEG3350 -- 0.1M bis-tris pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.6854.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.612α = 90
b = 183.969β = 108.124
c = 100.947γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2019-10-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9762DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.5183.8499.218.62.795510
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.550.61

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-VALUE5LB52.595.93890975440799.3710.2380.23560.280679.866
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]
0.817-2.8861.73-0.541
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.553
r_lrange_other18.155
r_lrange_it18.154
r_dihedral_angle_3_deg16.321
r_dihedral_angle_4_deg16.143
r_mcangle_it11.838
r_mcangle_other11.837
r_scangle_it11.791
r_scangle_other11.791
r_mcbond_it8.053
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.553
r_lrange_other18.155
r_lrange_it18.154
r_dihedral_angle_3_deg16.321
r_dihedral_angle_4_deg16.143
r_mcangle_it11.838
r_mcangle_other11.837
r_scangle_it11.791
r_scangle_other11.791
r_mcbond_it8.053
r_mcbond_other8.047
r_scbond_it7.763
r_scbond_other7.763
r_dihedral_angle_1_deg6.464
r_angle_refined_deg1.411
r_angle_other_deg1.248
r_symmetry_nbd_refined0.401
r_nbd_other0.327
r_symmetry_xyhbond_nbd_refined0.304
r_nbd_refined0.202
r_symmetry_nbd_other0.178
r_xyhbond_nbd_refined0.166
r_nbtor_refined0.158
r_symmetry_xyhbond_nbd_other0.143
r_xyhbond_nbd_other0.124
r_ncsr_local_group_70.098
r_ncsr_local_group_110.097
r_ncsr_local_group_80.094
r_ncsr_local_group_120.094
r_ncsr_local_group_60.09
r_ncsr_local_group_40.088
r_ncsr_local_group_30.087
r_ncsr_local_group_20.085
r_ncsr_local_group_90.085
r_ncsr_local_group_100.083
r_ncsr_local_group_10.081
r_ncsr_local_group_50.081
r_symmetry_nbtor_other0.076
r_chiral_restr0.06
r_bond_refined_d0.006
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms17546
Nucleic Acid Atoms
Solvent Atoms95
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing