X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293Ammonium sulfate, Cadmium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.1160.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 180.701α = 90
b = 180.701β = 90
c = 180.701γ = 90
Symmetry
Space GroupF 4 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU JUPITER 2102008-11-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL38B11.0SPring-8BL38B1

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
11.8301000.08957.411.624004
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)
1.81.861000.3811.4

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1DAT1.821.322765122899.950.197120.195660.22526RANDOM20.797
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_deg35.17
r_dihedral_angle_4_deg23.442
r_dihedral_angle_3_deg14.917
r_dihedral_angle_1_deg4.706
r_scangle_it3.742
r_scbond_it2.46
r_mcangle_it1.468
r_angle_refined_deg1.252
r_mcbond_it0.996
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.17
r_dihedral_angle_4_deg23.442
r_dihedral_angle_3_deg14.917
r_dihedral_angle_1_deg4.706
r_scangle_it3.742
r_scbond_it2.46
r_mcangle_it1.468
r_angle_refined_deg1.252
r_mcbond_it0.996
r_nbtor_refined0.303
r_nbd_refined0.23
r_symmetry_vdw_refined0.204
r_metal_ion_refined0.168
r_xyhbond_nbd_refined0.159
r_symmetry_hbond_refined0.159
r_symmetry_metal_ion_refined0.121
r_chiral_restr0.094
r_bond_refined_d0.012
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1406
Nucleic Acid Atoms
Solvent Atoms167
Heterogen Atoms14

Software

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