X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2XDOPDB ENTRY 2XDO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17pH 7
Crystal Properties
Matthews coefficientSolvent content
2.4750.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.7α = 111.1
b = 79.96β = 90.41
c = 88γ = 92.96
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH SX-1652010-11-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.3BESSY14.3

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
12.3751.9893.50.097.32.66616649.7
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)
12.372.569.60.492.12.5

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 2XDO2.3751.9862850331493.460.219370.218380.23776RANDOM44.735
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]
3.38-0.02-0.830.40.4-3.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.437
r_dihedral_angle_4_deg20.016
r_dihedral_angle_3_deg17.537
r_dihedral_angle_1_deg6.909
r_scangle_it3.479
r_scbond_it2.179
r_angle_refined_deg1.825
r_mcangle_it1.322
r_angle_other_deg1.147
r_mcbond_it0.711
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.437
r_dihedral_angle_4_deg20.016
r_dihedral_angle_3_deg17.537
r_dihedral_angle_1_deg6.909
r_scangle_it3.479
r_scbond_it2.179
r_angle_refined_deg1.825
r_mcangle_it1.322
r_angle_other_deg1.147
r_mcbond_it0.711
r_mcbond_other0.172
r_chiral_restr0.128
r_bond_refined_d0.02
r_gen_planes_refined0.008
r_bond_other_d0.004
r_gen_planes_other0.003
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 Atoms11346
Nucleic Acid Atoms
Solvent Atoms197
Heterogen Atoms396

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALEPACKdata scaling