X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3PUG 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP298magnesium chloride, glyoxylate, Tris, KCl, ammonium acetate, PEG 4500, glycerol, sodium acetate trihydrate
Crystal Properties
Matthews coefficientSolvent content
3.3763.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 155.353α = 90
b = 155.353β = 90
c = 139.412γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVRigaku Varimax-HR2009-03-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54

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
12.196.8199.50.10313.23.735791
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)
12.12.181000.3743.6

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 REPLACEMENTTHROUGHOUT3PUG2.196.8135791188099.220.184770.183080.21668RANDOM48.764
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.434
r_dihedral_angle_3_deg16.214
r_dihedral_angle_4_deg15.826
r_long_range_B_refined9.256
r_long_range_B_other9.229
r_scangle_other7.332
r_dihedral_angle_1_deg6.643
r_mcangle_it5.38
r_mcangle_other5.379
r_scbond_it5.293
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.434
r_dihedral_angle_3_deg16.214
r_dihedral_angle_4_deg15.826
r_long_range_B_refined9.256
r_long_range_B_other9.229
r_scangle_other7.332
r_dihedral_angle_1_deg6.643
r_mcangle_it5.38
r_mcangle_other5.379
r_scbond_it5.293
r_scbond_other5.282
r_mcbond_it4.304
r_mcbond_other4.302
r_angle_refined_deg1.916
r_angle_other_deg0.944
r_chiral_restr0.114
r_bond_refined_d0.02
r_gen_planes_refined0.011
r_gen_planes_other0.002
r_bond_other_d0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2795
Nucleic Acid Atoms
Solvent Atoms254
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PHASERphasing
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing