X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2Y8BPDB ENTRY 2Y8B

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.0540.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.225α = 90
b = 70.225β = 90
c = 47.027γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-3MAX III911-3

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
11.43096.60.079.13.54364912.8
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)
11.41.4886.80.162

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 2Y8B1.42541427219696.440.119690.117760.15636RANDOM14.582
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]
-0.08-0.080.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.635
r_sphericity_free29.736
r_dihedral_angle_4_deg19.094
r_dihedral_angle_3_deg11.44
r_sphericity_bonded11.366
r_dihedral_angle_1_deg6.644
r_rigid_bond_restr5.495
r_angle_refined_deg1.52
r_angle_other_deg1.101
r_chiral_restr0.322
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.635
r_sphericity_free29.736
r_dihedral_angle_4_deg19.094
r_dihedral_angle_3_deg11.44
r_sphericity_bonded11.366
r_dihedral_angle_1_deg6.644
r_rigid_bond_restr5.495
r_angle_refined_deg1.52
r_angle_other_deg1.101
r_chiral_restr0.322
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d0.006
r_gen_planes_other0.002
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_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1710
Nucleic Acid Atoms
Solvent Atoms258
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
PHASERphasing