X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1U6D 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION8.5277100 mM TrisHCl 200 mM MgCl2 30% PEG 4000, pH 8.5, VAPOR DIFFUSION, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.346.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.757α = 90
b = 92.069β = 90
c = 46.314γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 4.2.21.23983ALS4.2.2

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
11.536.494.70.07711.16.350551
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)
11.51.5564.60.4562.13.3

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1U6D1.5365055147967257694.660.180480.179480.19867RANDOM18.535
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]
0.07-0.80.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.462
r_dihedral_angle_4_deg20.823
r_dihedral_angle_3_deg10.892
r_dihedral_angle_1_deg6.559
r_scangle_it2.695
r_scbond_it1.869
r_angle_refined_deg1.211
r_mcangle_it1.175
r_mcbond_it0.724
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.462
r_dihedral_angle_4_deg20.823
r_dihedral_angle_3_deg10.892
r_dihedral_angle_1_deg6.559
r_scangle_it2.695
r_scbond_it1.869
r_angle_refined_deg1.211
r_mcangle_it1.175
r_mcbond_it0.724
r_nbtor_refined0.302
r_symmetry_vdw_refined0.241
r_nbd_refined0.194
r_symmetry_hbond_refined0.126
r_xyhbond_nbd_refined0.105
r_chiral_restr0.088
r_bond_refined_d0.009
r_gen_planes_refined0.005
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 Atoms2300
Nucleic Acid Atoms
Solvent Atoms333
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
d*TREKdata scaling
MOLREPphasing