X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DAT 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293Ammonium sulphate, Cadmium sulphate
Crystal Properties
Matthews coefficientSolvent content
3.1560.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 181.606α = 90
b = 181.606β = 90
c = 181.606γ = 90
Symmetry
Space GroupF 4 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102018-12-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B11SPring-8BL26B1

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
11.5830.0199.50.07661.99.235456
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)
11.581.610.246

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 REPLACEMENTTHROUGHOUT1DAT1.5827.7133626182199.420.167790.167040.18186RANDOM15.799
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_deg31.947
r_dihedral_angle_4_deg19.633
r_dihedral_angle_3_deg13.066
r_long_range_B_refined5.482
r_long_range_B_other5.33
r_dihedral_angle_1_deg4.896
r_scangle_other4.74
r_scbond_it3.092
r_scbond_other3.079
r_mcangle_other2.501
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.947
r_dihedral_angle_4_deg19.633
r_dihedral_angle_3_deg13.066
r_long_range_B_refined5.482
r_long_range_B_other5.33
r_dihedral_angle_1_deg4.896
r_scangle_other4.74
r_scbond_it3.092
r_scbond_other3.079
r_mcangle_other2.501
r_mcangle_it2.498
r_angle_refined_deg1.882
r_mcbond_it1.763
r_mcbond_other1.748
r_angle_other_deg1.626
r_chiral_restr0.098
r_bond_refined_d0.014
r_gen_planes_refined0.011
r_bond_other_d0.001
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 Atoms1360
Nucleic Acid Atoms
Solvent Atoms170
Heterogen Atoms11

Software

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