X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2XYS 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5293Reservoir buffer: 20 % PEG3350 0.2 M Mg formate Protein buffer: 50 mM trism 250 mM NaCl Ph 7.5, 0.5 mM strychnine
Crystal Properties
Matthews coefficientSolvent content
2.6854.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 130.9α = 90
b = 130.9β = 90
c = 190.139γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray150CCDADSC QUANTUM 315r2015-12-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.97627ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
13.272.8598.70.2120.9918.38.15928651.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.23.2998.51.0730.6912.37.3

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 REPLACEMENTTHROUGHOUT2xys3.272.8556374291098.580.18980.187640.23053RANDOM77.086
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]
2.811.412.81-9.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.341
r_dihedral_angle_3_deg18.865
r_long_range_B_refined17.661
r_long_range_B_other17.661
r_dihedral_angle_4_deg16.132
r_scangle_other14.029
r_mcangle_it13.441
r_mcangle_other13.441
r_scbond_it9.451
r_scbond_other9.448
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.341
r_dihedral_angle_3_deg18.865
r_long_range_B_refined17.661
r_long_range_B_other17.661
r_dihedral_angle_4_deg16.132
r_scangle_other14.029
r_mcangle_it13.441
r_mcangle_other13.441
r_scbond_it9.451
r_scbond_other9.448
r_mcbond_it8.915
r_mcbond_other8.913
r_dihedral_angle_1_deg8.443
r_angle_refined_deg2.053
r_angle_other_deg1.111
r_chiral_restr0.103
r_bond_refined_d0.017
r_gen_planes_refined0.01
r_bond_other_d0.006
r_gen_planes_other0.002
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 Atoms24623
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms386

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing