X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293Ammonium sulfate, Cadmium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.1460.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 181.594α = 90
b = 181.594β = 90
c = 181.594γ = 90
Symmetry
Space GroupF 4 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-03-03MSINGLE WAVELENGTH
21100CCDADSC QUANTUM 3152006-03-03
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU0.5086SPring-8BL41XU
2SYNCHROTRONSPRING-8 BEAMLINE BL41XU0.4639SPring-8BL41XU

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
12.5501000.09233.911.69397-339.084
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)
2.52.691000.3027.211.8

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 REPLACEMENTTHROUGHOUT1DAT2.545.41889450399.960.222980.219430.28671RANDOM31.593
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_deg39.964
r_dihedral_angle_4_deg27.738
r_dihedral_angle_3_deg21.981
r_sphericity_free19.109
r_dihedral_angle_1_deg11.829
r_scangle_it6.356
r_scbond_it4.155
r_mcangle_it2.451
r_angle_refined_deg2.262
r_mcbond_it1.495
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.964
r_dihedral_angle_4_deg27.738
r_dihedral_angle_3_deg21.981
r_sphericity_free19.109
r_dihedral_angle_1_deg11.829
r_scangle_it6.356
r_scbond_it4.155
r_mcangle_it2.451
r_angle_refined_deg2.262
r_mcbond_it1.495
r_nbtor_refined0.315
r_symmetry_hbond_refined0.307
r_metal_ion_refined0.305
r_nbd_refined0.274
r_symmetry_vdw_refined0.225
r_chiral_restr0.202
r_xyhbond_nbd_refined0.162
r_bond_refined_d0.026
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1366
Nucleic Acid Atoms
Solvent Atoms44
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing