X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6HL2chains A and B were placed two times independepently in the asymmetric unit

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.12810.1 M Tris pH 7.1, 0.85 M Na3-citrate, 0.1 M NaCl
Crystal Properties
Matthews coefficientSolvent content
2.6653.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.072α = 90
b = 113.397β = 90
c = 189.555γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-09-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.9724ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.548.197.30.0990.9885.63.747026
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.590.4670.769

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2.547.43446977229196.5160.210.20760.2494Random selection31.479
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]
0.9790.025-1.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.441
r_dihedral_angle_6_deg13.127
r_dihedral_angle_other_3_deg13.025
r_dihedral_angle_2_deg8.791
r_dihedral_angle_1_deg6.118
r_lrange_it3.995
r_lrange_other3.968
r_scangle_it1.595
r_scangle_other1.595
r_angle_refined_deg1.455
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.441
r_dihedral_angle_6_deg13.127
r_dihedral_angle_other_3_deg13.025
r_dihedral_angle_2_deg8.791
r_dihedral_angle_1_deg6.118
r_lrange_it3.995
r_lrange_other3.968
r_scangle_it1.595
r_scangle_other1.595
r_angle_refined_deg1.455
r_mcangle_it1.392
r_mcangle_other1.392
r_scbond_it0.921
r_scbond_other0.921
r_mcbond_it0.785
r_mcbond_other0.783
r_angle_other_deg0.496
r_nbd_other0.236
r_nbd_refined0.199
r_symmetry_nbd_other0.197
r_symmetry_nbd_refined0.192
r_nbtor_refined0.18
r_xyhbond_nbd_refined0.157
r_symmetry_xyhbond_nbd_refined0.109
r_symmetry_nbtor_other0.077
r_chiral_restr0.068
r_metal_ion_refined0.063
r_symmetry_xyhbond_nbd_other0.032
r_chiral_restr_other0.021
r_bond_refined_d0.006
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9072
Nucleic Acid Atoms
Solvent Atoms351
Heterogen Atoms126

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing