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
2.2545.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.91α = 90
b = 101.91β = 90
c = 120.47γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS2008-10-26MSINGLE 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
123099.80.18717.314.54339743397
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)
122.199.90.8595.214.55784

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 2IGO229.24142041420199099.890.158420.158420.156430.19956RANDOM11.138
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]
-0.29-0.290.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.606
r_dihedral_angle_4_deg14.494
r_dihedral_angle_3_deg13.618
r_dihedral_angle_1_deg6.875
r_scangle_it3.871
r_scbond_it2.843
r_angle_refined_deg1.861
r_mcangle_it1.694
r_mcbond_it1.393
r_angle_other_deg1.011
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.606
r_dihedral_angle_4_deg14.494
r_dihedral_angle_3_deg13.618
r_dihedral_angle_1_deg6.875
r_scangle_it3.871
r_scbond_it2.843
r_angle_refined_deg1.861
r_mcangle_it1.694
r_mcbond_it1.393
r_angle_other_deg1.011
r_mcbond_other0.303
r_symmetry_vdw_refined0.258
r_symmetry_vdw_other0.231
r_nbd_refined0.224
r_nbd_other0.214
r_chiral_restr0.196
r_nbtor_refined0.182
r_symmetry_hbond_refined0.16
r_xyhbond_nbd_refined0.139
r_nbtor_other0.093
r_bond_refined_d0.022
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
r_xyhbond_nbd_other
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 Atoms4517
Nucleic Acid Atoms
Solvent Atoms307
Heterogen Atoms65

Software

Software
Software NamePurpose
MAR345data collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling