X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1H9Z 
experimental modelPDB 6HSC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8292.05M NaCl, 10% PEG 4000 and 0.05 Tris pH=8.0
Crystal Properties
Matthews coefficientSolvent content
2.3948.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.26α = 74.35
b = 92.128β = 89.29
c = 95.553γ = 79.98
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2022-02-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.97625ESRFID30B

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
1246.0289.10.058160.082240.051860.94518.111.57440941.82
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)
122.07184.480.25890.36610.25890.861.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6HSC246.0270736363489.010.22280.220310.27066RANDOM39.111
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]
-0.02-0.03-0.080.69-0.7-0.97
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.696
r_dihedral_angle_4_deg20.807
r_dihedral_angle_3_deg17.088
r_dihedral_angle_1_deg6.778
r_long_range_B_other6.592
r_long_range_B_refined6.591
r_scangle_other5.182
r_mcangle_it4.003
r_mcangle_other4.003
r_scbond_it3.416
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.696
r_dihedral_angle_4_deg20.807
r_dihedral_angle_3_deg17.088
r_dihedral_angle_1_deg6.778
r_long_range_B_other6.592
r_long_range_B_refined6.591
r_scangle_other5.182
r_mcangle_it4.003
r_mcangle_other4.003
r_scbond_it3.416
r_scbond_other3.411
r_mcbond_it2.856
r_mcbond_other2.853
r_angle_refined_deg1.948
r_angle_other_deg1.525
r_chiral_restr0.096
r_bond_refined_d0.013
r_gen_planes_refined0.01
r_bond_other_d0.003
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8896
Nucleic Acid Atoms
Solvent Atoms91
Heterogen Atoms172

Software

Software
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction
Aimlessdata scaling
PHENIXphasing