X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3MHYPDB ENTRY 3MHY and 3G9D
experimental modelPDB 3G9DPDB ENTRY 3MHY and 3G9D

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529812% PEG 8000, 0.2M Nacl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.0459.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 115.654α = 90
b = 115.654β = 90
c = 105.626γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2010-02-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.09700.0660.06613.752.68017131022
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.092.297.70.210.2053.92.6

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3MHY and 3G9D2.09702947015511000.153150.151130.19108RANDOM25.288
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]
-0.22-0.11-0.220.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.475
r_dihedral_angle_4_deg19.141
r_dihedral_angle_3_deg15.896
r_scangle_it5.451
r_dihedral_angle_1_deg5.356
r_scbond_it3.553
r_mcangle_it1.953
r_angle_refined_deg1.843
r_mcbond_it1.111
r_chiral_restr0.138
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.475
r_dihedral_angle_4_deg19.141
r_dihedral_angle_3_deg15.896
r_scangle_it5.451
r_dihedral_angle_1_deg5.356
r_scbond_it3.553
r_mcangle_it1.953
r_angle_refined_deg1.843
r_mcbond_it1.111
r_chiral_restr0.138
r_bond_refined_d0.023
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3027
Nucleic Acid Atoms
Solvent Atoms393
Heterogen Atoms29

Software

Software
Software NamePurpose
PHENIXrefinement
REFMACrefinement