X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1SDZ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.4291100mM Bis-Tris pH 5.4, 0.2M (NH4)2SO4, 3%( vol/vol) CH3OH, 22% (wt/vol) Polyethylene Glycol 3350 , VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.1442.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.782α = 90
b = 99.782β = 90
c = 71.344γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2009-07-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XUSPring-8BL41XU

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
12.45099.43088011.52.3

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 REPLACEMENTTHROUGHOUT1SDZ2.432.9829236162299.330.149590.145750.21709RANDOM29.7
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]
7.837.83-15.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.179
r_dihedral_angle_3_deg24.359
r_dihedral_angle_4_deg19.789
r_dihedral_angle_1_deg12.107
r_scangle_it4.733
r_scbond_it3.611
r_mcangle_it2.091
r_mcbond_it1.366
r_angle_refined_deg0.99
r_chiral_restr0.083
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.179
r_dihedral_angle_3_deg24.359
r_dihedral_angle_4_deg19.789
r_dihedral_angle_1_deg12.107
r_scangle_it4.733
r_scbond_it3.611
r_mcangle_it2.091
r_mcbond_it1.366
r_angle_refined_deg0.99
r_chiral_restr0.083
r_gen_planes_refined0.02
r_bond_refined_d0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4790
Nucleic Acid Atoms
Solvent Atoms4
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement