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
3.0159.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 149.053α = 90
b = 149.053β = 90
c = 131.833γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 92mirrors2011-04-25MSINGLE 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
12.245093.976070714701

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 4LY92.2436.3271470378693.890.221820.21920.27037RANDOM47.628
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]
-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.85
r_dihedral_angle_4_deg21.782
r_dihedral_angle_3_deg17.825
r_long_range_B_refined8.43
r_long_range_B_other8.43
r_dihedral_angle_1_deg6.921
r_scangle_other6.345
r_mcangle_it5.741
r_mcangle_other5.741
r_scbond_it4.394
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.85
r_dihedral_angle_4_deg21.782
r_dihedral_angle_3_deg17.825
r_long_range_B_refined8.43
r_long_range_B_other8.43
r_dihedral_angle_1_deg6.921
r_scangle_other6.345
r_mcangle_it5.741
r_mcangle_other5.741
r_scbond_it4.394
r_scbond_other4.327
r_mcbond_it4.035
r_mcbond_other4.034
r_angle_refined_deg1.849
r_angle_other_deg0.898
r_chiral_restr0.103
r_bond_refined_d0.016
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 Atoms179
Heterogen Atoms137

Software

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