X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2IGOpdb entry 2IGO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.22980.1M MES, 50MM MGCL2, 10% (W/V)% MONOMETHYLETHER PEG 2000, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2545.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.059α = 90
b = 102.059β = 90
c = 119.693γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS2008-12-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-21.0379MAX III911-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.63099.90.118.112.98354883548
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.799.60.863.19.913637

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 2IGO1.6308158781587196199.880.185560.185560.184880.2129RANDOM12.416
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]
-0.49-0.490.97
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.291
r_dihedral_angle_4_deg16.281
r_dihedral_angle_3_deg12.474
r_dihedral_angle_1_deg6.871
r_scangle_it3.699
r_scbond_it2.739
r_angle_refined_deg1.841
r_mcangle_it1.663
r_mcbond_it1.426
r_angle_other_deg1.011
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.291
r_dihedral_angle_4_deg16.281
r_dihedral_angle_3_deg12.474
r_dihedral_angle_1_deg6.871
r_scangle_it3.699
r_scbond_it2.739
r_angle_refined_deg1.841
r_mcangle_it1.663
r_mcbond_it1.426
r_angle_other_deg1.011
r_mcbond_other0.363
r_symmetry_vdw_other0.261
r_symmetry_vdw_refined0.252
r_nbd_refined0.235
r_xyhbond_nbd_other0.223
r_nbd_other0.213
r_nbtor_refined0.185
r_chiral_restr0.161
r_xyhbond_nbd_refined0.156
r_symmetry_hbond_refined0.119
r_nbtor_other0.092
r_bond_refined_d0.02
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.001
r_metal_ion_refined
r_metal_ion_other
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 Atoms4531
Nucleic Acid Atoms
Solvent Atoms436
Heterogen Atoms53

Software

Software
Software NamePurpose
MAR345data collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling