X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherinhouse structure of SeMet- mutant

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2930.095M sodium citrate tribasic dihydrate, pH 5.6-6.4, 19% v/v 2-propanol, 19% polyethylene glycol 4000, 5% v/v glycerol ZnCl2
Crystal Properties
Matthews coefficientSolvent content
2.5852.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 367.696α = 90
b = 99.079β = 109.61
c = 131.337γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2014-04-14MSINGLE WAVELENGTH
21x-ray100CCDADSC QUANTUM 3152010-12-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-11.265ESRFID23-1
2SYNCHROTRONESRF BEAMLINE ID14-40.9736, 2.13ESRFID14-4

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
12.2710093.612.22.66183046

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 REPLACEMENTTHROUGHOUTinhouse structure of SeMet- mutant2.27123.72183046963994.470.202340.200950.22864RANDOM49.423
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.986
r_dihedral_angle_4_deg22.334
r_dihedral_angle_3_deg16.235
r_long_range_B_refined9.036
r_long_range_B_other9.029
r_scangle_other6.965
r_dihedral_angle_1_deg6.075
r_mcangle_other5.799
r_mcangle_it5.798
r_scbond_it4.596
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.986
r_dihedral_angle_4_deg22.334
r_dihedral_angle_3_deg16.235
r_long_range_B_refined9.036
r_long_range_B_other9.029
r_scangle_other6.965
r_dihedral_angle_1_deg6.075
r_mcangle_other5.799
r_mcangle_it5.798
r_scbond_it4.596
r_scbond_other4.596
r_mcbond_it4.047
r_mcbond_other4.045
r_angle_refined_deg1.548
r_angle_other_deg1.297
r_chiral_restr0.09
r_bond_refined_d0.013
r_gen_planes_refined0.009
r_bond_other_d0.008
r_gen_planes_other0.006
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 Atoms28776
Nucleic Acid Atoms
Solvent Atoms602
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SHARPphasing
XSCALEdata scaling