X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3Q6X 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.22920.2M NaCl, 0.1M Phosphate/citrate pH 4.2, 20% w/v PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.1943.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.929α = 90
b = 122.929β = 90
c = 38.501γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2017-06-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.72931BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim 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
11.4361.4699.80.0830.0880.9916.59.2120161-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.431.5298.80.7380.7820.712.69.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3q6x1.4361.46117209300499.820.074610.073510.11632RANDOM20.072
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]
-3.26-3.266.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.647
r_dihedral_angle_4_deg20.607
r_rigid_bond_restr18.943
r_dihedral_angle_3_deg12.557
r_scbond_it11.336
r_scbond_other11.334
r_scangle_other8.173
r_long_range_B_refined7.906
r_long_range_B_other7.905
r_dihedral_angle_1_deg7.086
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.647
r_dihedral_angle_4_deg20.607
r_rigid_bond_restr18.943
r_dihedral_angle_3_deg12.557
r_scbond_it11.336
r_scbond_other11.334
r_scangle_other8.173
r_long_range_B_refined7.906
r_long_range_B_other7.905
r_dihedral_angle_1_deg7.086
r_mcbond_it5.766
r_mcbond_other5.753
r_mcangle_it5.36
r_mcangle_other5.36
r_angle_refined_deg1.758
r_angle_other_deg1.586
r_chiral_restr0.102
r_bond_refined_d0.014
r_gen_planes_refined0.011
r_bond_other_d0.002
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_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5081
Nucleic Acid Atoms
Solvent Atoms778
Heterogen Atoms99

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing