X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4V2YPDB ENTRY 4V2Y

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
164 MM SODIUM CITRATE PH 7.0, 100 MM HEPES PH 7.0, 10 %(W/V) PEG 5000 MME
Crystal Properties
Matthews coefficientSolvent content
3.868

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 137.86α = 90
b = 137.86β = 90
c = 154.39γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2011-06-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SASLSX10SA

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
12.93999.10.110.532.9719746-3
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)
12.93.0798.30.532.222.95

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 4V2Y2.938.981877698999.650.176640.174520.21688RANDOM48.624
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]
-0.65-0.32-0.652.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.633
r_dihedral_angle_3_deg19.674
r_dihedral_angle_4_deg14.071
r_dihedral_angle_1_deg7.979
r_mcangle_it2.846
r_scbond_it2.144
r_angle_refined_deg1.952
r_mcbond_it1.759
r_mcbond_other1.758
r_angle_other_deg1.038
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.633
r_dihedral_angle_3_deg19.674
r_dihedral_angle_4_deg14.071
r_dihedral_angle_1_deg7.979
r_mcangle_it2.846
r_scbond_it2.144
r_angle_refined_deg1.952
r_mcbond_it1.759
r_mcbond_other1.758
r_angle_other_deg1.038
r_chiral_restr0.089
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d0.001
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 Atoms3308
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing