X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4B8WPDB ENTRY 4B8W

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.1M BIS-TRIS-PROPANE PH 7.5, 0.15M SODIUM CHLORIDE, 25% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.1743.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.407α = 72.54
b = 90.478β = 72.64
c = 147.518γ = 60.14
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-09-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04DiamondI04

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
12.629.6497.40.1461.22.11139983.342.5
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)
12.62.6478.11.153.32.1

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 4B8W2.629.66107442565396.680.224820.221630.28565RANDOM45.598
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]
-0.710.2-0.370.27-0.30.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.711
r_dihedral_angle_4_deg16.524
r_dihedral_angle_3_deg15.449
r_dihedral_angle_1_deg6.553
r_mcangle_it2.338
r_mcbond_it1.43
r_mcbond_other1.43
r_angle_refined_deg1.38
r_scbond_it1.324
r_angle_other_deg0.816
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.711
r_dihedral_angle_4_deg16.524
r_dihedral_angle_3_deg15.449
r_dihedral_angle_1_deg6.553
r_mcangle_it2.338
r_mcbond_it1.43
r_mcbond_other1.43
r_angle_refined_deg1.38
r_scbond_it1.324
r_angle_other_deg0.816
r_chiral_restr0.069
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms28839
Nucleic Acid Atoms
Solvent Atoms41
Heterogen Atoms1036

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing