X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1QBKPDB ENTRY 1QBK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.62930.1M Tris-HCl pH 8.6, 14% (w/v) PEG 8000, 0.1M NaH2PO4, 0.015mM Phenol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.7667.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 132.306α = 90
b = 169.805β = 90
c = 68.458γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152005-07-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.0000SPring-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
13.25094.90.07113.22519023669
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)
13.23.3182.80.4343.6

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 1QBK3.247.5723669126594.950.237650.235510.27859RANDOM129.703
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]
-10.3515.29-4.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.253
r_dihedral_angle_3_deg18.72
r_dihedral_angle_4_deg18.174
r_dihedral_angle_1_deg4.569
r_angle_refined_deg1.112
r_scangle_it0.858
r_mcangle_it0.512
r_scbond_it0.496
r_nbtor_refined0.302
r_mcbond_it0.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.253
r_dihedral_angle_3_deg18.72
r_dihedral_angle_4_deg18.174
r_dihedral_angle_1_deg4.569
r_angle_refined_deg1.112
r_scangle_it0.858
r_mcangle_it0.512
r_scbond_it0.496
r_nbtor_refined0.302
r_mcbond_it0.28
r_nbd_refined0.218
r_symmetry_vdw_refined0.173
r_xyhbond_nbd_refined0.134
r_chiral_restr0.08
r_symmetry_hbond_refined0.07
r_bond_refined_d0.009
r_gen_planes_refined0.003
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_refined
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_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6689
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing