X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2V8W 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2890.01M Tri-sodium citrate, 16% PEG 6000
Crystal Properties
Matthews coefficientSolvent content
2.3848.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.595α = 90
b = 140.394β = 104.037
c = 61.961γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2019-07-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX10.953700Australian SynchrotronMX1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)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
12.4670.19799.90.1773.67.728611
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.462.590.8760.9

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-VALUE2V8W2.4646.21628587145099.8710.2520.250.291834.813
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]
0.0680.896-2.7431.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.797
r_dihedral_angle_3_deg13.835
r_dihedral_angle_4_deg13.569
r_dihedral_angle_1_deg6.66
r_lrange_it3.227
r_lrange_other3.186
r_mcangle_it2.107
r_mcangle_other2.107
r_scangle_it1.665
r_scangle_other1.665
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.797
r_dihedral_angle_3_deg13.835
r_dihedral_angle_4_deg13.569
r_dihedral_angle_1_deg6.66
r_lrange_it3.227
r_lrange_other3.186
r_mcangle_it2.107
r_mcangle_other2.107
r_scangle_it1.665
r_scangle_other1.665
r_angle_refined_deg1.185
r_mcbond_it1.175
r_mcbond_other1.175
r_angle_other_deg1.076
r_scbond_it0.933
r_scbond_other0.933
r_symmetry_xyhbond_nbd_refined0.225
r_symmetry_nbd_other0.168
r_nbd_refined0.162
r_nbtor_refined0.152
r_xyhbond_nbd_refined0.147
r_symmetry_nbd_refined0.134
r_nbd_other0.133
r_symmetry_nbtor_other0.072
r_chiral_restr0.037
r_gen_planes_refined0.003
r_bond_refined_d0.002
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4817
Nucleic Acid Atoms
Solvent Atoms102
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing