X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YZ1PDB ENTRY 1YZ1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.22770.1M Tris, pH 8.2, 22% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal Properties
Matthews coefficientSolvent content
2.754.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.192α = 90
b = 81.543β = 90
c = 139.92γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102008-05-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.0000Photon FactoryAR-NW12A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.65097.50.0960.09613.642818827483
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.62.6997.50.4670.4672.93.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1YZ12.6362681226115136697.40.238830.238830.236570.28031RANDOM55.88
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]
-2.247.4-5.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.026
r_dihedral_angle_4_deg18.239
r_dihedral_angle_3_deg15.131
r_scangle_it6.503
r_dihedral_angle_1_deg4.505
r_mcangle_it4.263
r_scbond_it4.078
r_rigid_bond_restr3.453
r_mcbond_it3.118
r_sphericity_free1.227
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.026
r_dihedral_angle_4_deg18.239
r_dihedral_angle_3_deg15.131
r_scangle_it6.503
r_dihedral_angle_1_deg4.505
r_mcangle_it4.263
r_scbond_it4.078
r_rigid_bond_restr3.453
r_mcbond_it3.118
r_sphericity_free1.227
r_sphericity_bonded1.004
r_angle_refined_deg0.897
r_nbtor_refined0.298
r_symmetry_vdw_refined0.228
r_nbd_refined0.193
r_symmetry_hbond_refined0.175
r_xyhbond_nbd_refined0.124
r_chiral_restr0.068
r_bond_refined_d0.009
r_gen_planes_refined0.002
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4788
Nucleic Acid Atoms
Solvent Atoms37
Heterogen Atoms

Software

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