X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.1 M sodium citrate pH 5.0, 14% (w/v) PEG 6000
Crystal Properties
Matthews coefficientSolvent content
2.6653.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.87α = 90
b = 104.137β = 90
c = 113.988γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2019-02-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97950DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.3479.8998.90.0580.0220.99913.47.6210296
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.341.371.2150.6070.5651.1

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-VALUE5bwi1.3477.0022099581058298.6510.1770.17620.198921.494
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]
0.946-0.041-0.905
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.298
r_dihedral_angle_4_deg16.709
r_dihedral_angle_3_deg12.485
r_dihedral_angle_1_deg6.785
r_lrange_it5.531
r_lrange_other5.308
r_scangle_it3.868
r_scangle_other3.868
r_mcangle_other2.739
r_mcangle_it2.737
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.298
r_dihedral_angle_4_deg16.709
r_dihedral_angle_3_deg12.485
r_dihedral_angle_1_deg6.785
r_lrange_it5.531
r_lrange_other5.308
r_scangle_it3.868
r_scangle_other3.868
r_mcangle_other2.739
r_mcangle_it2.737
r_scbond_it2.63
r_scbond_other2.63
r_mcbond_it1.945
r_mcbond_other1.933
r_angle_refined_deg1.807
r_angle_other_deg1.555
r_nbd_other0.267
r_symmetry_xyhbond_nbd_refined0.243
r_nbd_refined0.218
r_xyhbond_nbd_refined0.179
r_symmetry_nbd_refined0.178
r_symmetry_nbd_other0.175
r_nbtor_refined0.171
r_chiral_restr0.095
r_symmetry_nbtor_other0.084
r_ncsr_local_group_10.084
r_bond_refined_d0.014
r_gen_planes_refined0.01
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6282
Nucleic Acid Atoms
Solvent Atoms992
Heterogen Atoms78

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
REFMACphasing