X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4LY9PDB ENTRY 4LY9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52980.1M Bis-tris, 0.2M NaI, 16%PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.0259.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 149.181α = 90
b = 149.181β = 90
c = 132.327γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 92osmic mirrors2011-08-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.45091612601

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 4LY92.437.9761260326999.10.218010.215080.27248RANDOM49.594
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]
0.010.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.658
r_dihedral_angle_4_deg20.381
r_dihedral_angle_3_deg18.009
r_long_range_B_refined8.412
r_long_range_B_other8.412
r_dihedral_angle_1_deg6.955
r_scangle_other6.225
r_mcangle_it5.992
r_mcangle_other5.991
r_scbond_it4.171
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.658
r_dihedral_angle_4_deg20.381
r_dihedral_angle_3_deg18.009
r_long_range_B_refined8.412
r_long_range_B_other8.412
r_dihedral_angle_1_deg6.955
r_scangle_other6.225
r_mcangle_it5.992
r_mcangle_other5.991
r_scbond_it4.171
r_scbond_other4.105
r_mcbond_it4.023
r_mcbond_other4.02
r_angle_refined_deg1.734
r_angle_other_deg0.884
r_chiral_restr0.093
r_bond_refined_d0.014
r_gen_planes_refined0.008
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9075
Nucleic Acid Atoms
Solvent Atoms193
Heterogen Atoms143

Software

Software
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling