X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1XKKPDB ID 1XKK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.5293pH 6.5, hanging drop vapor diffusion, temperature 20K, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2545.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.806α = 90
b = 68.881β = 90
c = 104.558γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-07-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XUSPring-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
11.55097.80.048145.0253697
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)
11.51.5599.20.5832.44.58

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 ID 1XKK1.55050707271397.20.220.2190.243RANDOM36.52
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]
0.920.27-1.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg13.842
r_scangle_it6.088
r_dihedral_angle_1_deg5.271
r_scbond_it3.93
r_mcangle_it2.839
r_mcbond_it1.74
r_angle_refined_deg1.24
r_chiral_restr0.076
r_bond_refined_d0.01
r_gen_planes_refined0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg13.842
r_scangle_it6.088
r_dihedral_angle_1_deg5.271
r_scbond_it3.93
r_mcangle_it2.839
r_mcbond_it1.74
r_angle_refined_deg1.24
r_chiral_restr0.076
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2357
Nucleic Acid Atoms
Solvent Atoms126
Heterogen Atoms53

Software

Software
Software NamePurpose
d*TREKdata scaling
d*TREKdata reduction
MOLREPphasing
REFMACrefinement
Cootmodel building