X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3W7R 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72930.1M HEPES, 3.0 M ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
3.2962.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 248.808α = 90
b = 248.808β = 90
c = 248.808γ = 90
Symmetry
Space GroupI 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2015-11-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.90000SPring-8BL44XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
13.5501000.1325.69.332346
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.53.561000.852.628.3

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 REPLACEMENTTHROUGHOUT3W7R3.52029340149395.330.275860.271770.35881RANDOM47.361
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_deg40.308
r_dihedral_angle_3_deg20.688
r_dihedral_angle_4_deg16.872
r_dihedral_angle_1_deg9.314
r_long_range_B_refined3.601
r_long_range_B_other3.601
r_angle_refined_deg1.796
r_mcangle_it1.731
r_mcangle_other1.731
r_angle_other_deg1.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.308
r_dihedral_angle_3_deg20.688
r_dihedral_angle_4_deg16.872
r_dihedral_angle_1_deg9.314
r_long_range_B_refined3.601
r_long_range_B_other3.601
r_angle_refined_deg1.796
r_mcangle_it1.731
r_mcangle_other1.731
r_angle_other_deg1.13
r_scangle_other1.096
r_mcbond_it0.932
r_mcbond_other0.932
r_scbond_it0.556
r_scbond_other0.556
r_chiral_restr0.094
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.002
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 Atoms11285
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms168

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing