X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DDYPDB ENTRY 3DDY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.829320% (w/v) PEG 4000, 0.2M MgCl2, 100mM HEPES pH6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0840.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.288α = 90
b = 46.582β = 90
c = 161.053γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU JUPITER 210monochromator2008-08-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B11.00SPring-8BL26B1

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
11.42125.55958164

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 3DDY1.42120.1558164653397.120.196320.192060.23443RANDOM23.28
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_deg38.332
r_dihedral_angle_4_deg21.234
r_dihedral_angle_3_deg16.539
r_dihedral_angle_1_deg9.927
r_scangle_it5.998
r_scbond_it4.015
r_mcangle_it2.967
r_angle_refined_deg2.896
r_mcbond_it1.991
r_chiral_restr0.353
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.332
r_dihedral_angle_4_deg21.234
r_dihedral_angle_3_deg16.539
r_dihedral_angle_1_deg9.927
r_scangle_it5.998
r_scbond_it4.015
r_mcangle_it2.967
r_angle_refined_deg2.896
r_mcbond_it1.991
r_chiral_restr0.353
r_nbtor_refined0.327
r_symmetry_vdw_refined0.308
r_nbd_refined0.242
r_symmetry_hbond_refined0.204
r_xyhbond_nbd_refined0.16
r_bond_refined_d0.033
r_gen_planes_refined0.015
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2832
Nucleic Acid Atoms
Solvent Atoms405
Heterogen Atoms54

Software

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