X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2J8ZPDB ENTRY 2J8Z

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529830 % PEG 4000, 0.1 M Tris, 0.2 M sodium acetate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.7855.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.354α = 90
b = 184.359β = 90
c = 318.047γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 300 mm plateMirrors2005-06-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.54

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
1319.9488.7362093620945.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
133.262.5

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 2J8Z319.943425434254179588.630.221550.221550.219550.25968RANDOM40.61
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]
0.650.57-1.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.838
r_dihedral_angle_3_deg13.798
r_dihedral_angle_4_deg12.741
r_dihedral_angle_1_deg5.169
r_angle_refined_deg0.935
r_angle_other_deg0.783
r_scangle_it0.251
r_nbd_refined0.183
r_nbtor_refined0.166
r_scbond_it0.164
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.838
r_dihedral_angle_3_deg13.798
r_dihedral_angle_4_deg12.741
r_dihedral_angle_1_deg5.169
r_angle_refined_deg0.935
r_angle_other_deg0.783
r_scangle_it0.251
r_nbd_refined0.183
r_nbtor_refined0.166
r_scbond_it0.164
r_nbd_other0.162
r_symmetry_vdw_other0.152
r_symmetry_hbond_refined0.144
r_symmetry_vdw_refined0.143
r_xyhbond_nbd_refined0.119
r_mcangle_it0.091
r_nbtor_other0.08
r_mcbond_it0.069
r_chiral_restr0.049
r_mcbond_other0.016
r_bond_refined_d0.005
r_bond_other_d0.004
r_gen_planes_refined0.002
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12580
Nucleic Acid Atoms
Solvent Atoms3
Heterogen Atoms240

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing