X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DUTPDB ENTRY 1DUT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.50.1M IMIDAZOLEMALATE BUFFER PH 5.5, 30% (V/V) PEG600
Crystal Properties
Matthews coefficientSolvent content
2.1943

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.763α = 90
b = 102.763β = 90
c = 86.174γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2000-09-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
11.7488.9999.50.0624.55.7529062
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)
11.761.8940.452.32.8

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1DUT1.741049805267899.780.173720.171370.21857RANDOM23.266
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]
-0.79-0.39-0.791.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.819
r_dihedral_angle_3_deg15.515
r_dihedral_angle_4_deg14.515
r_dihedral_angle_1_deg6.598
r_scangle_it5.095
r_scbond_it3.322
r_mcangle_it2.034
r_angle_refined_deg1.91
r_mcbond_it1.198
r_angle_other_deg0.993
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.819
r_dihedral_angle_3_deg15.515
r_dihedral_angle_4_deg14.515
r_dihedral_angle_1_deg6.598
r_scangle_it5.095
r_scbond_it3.322
r_mcangle_it2.034
r_angle_refined_deg1.91
r_mcbond_it1.198
r_angle_other_deg0.993
r_mcbond_other0.42
r_chiral_restr0.125
r_bond_refined_d0.024
r_gen_planes_refined0.01
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4077
Nucleic Acid Atoms
Solvent Atoms477
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing