X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4DST 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2770.1 M, TrisCl, 0.2 M NaOAc and 30-35 % PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.3547.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.63α = 90
b = 78.63β = 90
c = 77.54γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2015-05-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.979DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.9839.3199.90.1520.1710.05411.210.112435
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)
11.982.031001.321.480.561.79.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4DST1.9839.311185158499.940.181550.178210.25183RANDOM37.222
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]
-0.53-0.26-0.531.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.522
r_dihedral_angle_4_deg16.434
r_dihedral_angle_3_deg14.547
r_long_range_B_refined6.942
r_long_range_B_other6.917
r_dihedral_angle_1_deg6.594
r_scangle_other4.967
r_mcangle_it4.628
r_mcangle_other4.626
r_scbond_it3.149
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.522
r_dihedral_angle_4_deg16.434
r_dihedral_angle_3_deg14.547
r_long_range_B_refined6.942
r_long_range_B_other6.917
r_dihedral_angle_1_deg6.594
r_scangle_other4.967
r_mcangle_it4.628
r_mcangle_other4.626
r_scbond_it3.149
r_scbond_other3.148
r_mcbond_it2.998
r_mcbond_other2.998
r_angle_refined_deg1.496
r_angle_other_deg0.945
r_chiral_restr0.081
r_bond_refined_d0.01
r_gen_planes_refined0.005
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1375
Nucleic Acid Atoms
Solvent Atoms81
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing