X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2XDT 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.52930.1M HEPES pH 7.5; 25% PEG 3350, VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3146.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.246α = 90
b = 132.816β = 90
c = 233.687γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2010-03-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.9778DiamondI24

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
133097.80.1535.836003260032-3-3
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)
133.1698.80.6681.638778

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 REPLACEMENTTHROUGHOUT2XDT319.996003256650301997.570.231330.231330.228570.28264RANDOM34.252
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]
3.32-1.74-1.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.351
r_dihedral_angle_4_deg17.299
r_dihedral_angle_3_deg15.324
r_scangle_it7.851
r_dihedral_angle_1_deg5.941
r_scbond_it5.549
r_mcangle_it3.888
r_mcbond_it2.109
r_angle_refined_deg1.087
r_angle_other_deg0.834
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.351
r_dihedral_angle_4_deg17.299
r_dihedral_angle_3_deg15.324
r_scangle_it7.851
r_dihedral_angle_1_deg5.941
r_scbond_it5.549
r_mcangle_it3.888
r_mcbond_it2.109
r_angle_refined_deg1.087
r_angle_other_deg0.834
r_mcbond_other0.314
r_chiral_restr0.073
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d0.002
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms17494
Nucleic Acid Atoms
Solvent Atoms39
Heterogen Atoms109

Software

Software
Software NamePurpose
GDAdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling