X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YZNpdb entries 1YZN, 1UKV
experimental modelPDB 1UKVpdb entries 1YZN, 1UKV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.529125% PEG3350, 0.2M magnesium chloride, 0.1M Tris, pH 8.5, vapor diffusion, sitting drop, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.346.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.79α = 90
b = 75.79β = 90
c = 49.08γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2006-01-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E1.5418

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
12.62301000.08810.65102
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)
12.622.711000.82610.5

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTpdb entries 1YZN, 1UKV2.63130504823399.980.2010.1990.252336.747
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]
-0.603-0.302-0.6030.905
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.02
r_dihedral_angle_4_deg24.925
r_dihedral_angle_3_deg16.052
r_dihedral_angle_1_deg4.754
r_scangle_it1.662
r_angle_refined_deg1.397
r_scbond_it0.99
r_angle_other_deg0.797
r_scangle_other0.753
r_mcangle_it0.599
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.02
r_dihedral_angle_4_deg24.925
r_dihedral_angle_3_deg16.052
r_dihedral_angle_1_deg4.754
r_scangle_it1.662
r_angle_refined_deg1.397
r_scbond_it0.99
r_angle_other_deg0.797
r_scangle_other0.753
r_mcangle_it0.599
r_mcbond_it0.459
r_scbond_other0.287
r_symmetry_vdw_other0.277
r_mcangle_other0.268
r_symmetry_hbond_refined0.227
r_nbd_refined0.223
r_nbd_other0.209
r_nbtor_refined0.191
r_xyhbond_nbd_refined0.19
r_symmetry_vdw_refined0.167
r_metal_ion_refined0.137
r_nbtor_other0.097
r_chiral_restr0.075
r_mcbond_other0.069
r_bond_refined_d0.019
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1240
Nucleic Acid Atoms
Solvent Atoms5
Heterogen Atoms31

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction