X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OO8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.6290JCSG+ screen e4: 1.26M ammonium sulphate: 200mM lithium sulphate, 100mM Tris pH 8.5: cryo: 25% EG in 3 steps
Crystal Properties
Matthews coefficientSolvent content
2.551

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.81α = 90
b = 63.81β = 90
c = 177.45γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2013-01-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.10.9774ALS5.0.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)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
12.0545.1299.50.0510.0610.99918.433.1834413337.11
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.052.1299.80.4780.01712.813.308

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 REPLACEMENTTHROUGHOUT2OO82.0545.1244082217399.580.1490.1480.166RANDOM36.96
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]
-1.9-1.93.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.919
r_dihedral_angle_4_deg16.585
r_dihedral_angle_3_deg13.605
r_dihedral_angle_1_deg6.379
r_angle_refined_deg1.335
r_angle_other_deg0.956
r_chiral_restr0.083
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.919
r_dihedral_angle_4_deg16.585
r_dihedral_angle_3_deg13.605
r_dihedral_angle_1_deg6.379
r_angle_refined_deg1.335
r_angle_other_deg0.956
r_chiral_restr0.083
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.005
r_gen_planes_other0.005
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4420
Nucleic Acid Atoms
Solvent Atoms231
Heterogen Atoms102

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing
Cootmodel building