X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1XWSPDB ENTRY 1XWS

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP1.5 UL SITTING DROPS, 1.6 M SODIUM-POTASSIUM PHOSPHATE, 0.1 M HEPES PH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.6353.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 153.07α = 90
b = 153.07β = 90
c = 78.6γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS2006-03-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SASLSX10SA

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
12.844.1999.70.0611.232.9168542
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)
12.82.91000.382.212.9

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 1XWS2.876.471581883498.50.2440.2420.289RANDOM20.47
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]
-5.73-2.87-5.738.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.2
r_dihedral_angle_3_deg18.296
r_dihedral_angle_4_deg14.179
r_dihedral_angle_1_deg5.846
r_angle_refined_deg1.265
r_scangle_it1.256
r_angle_other_deg0.923
r_scbond_it0.793
r_mcangle_it0.699
r_mcbond_it0.423
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.2
r_dihedral_angle_3_deg18.296
r_dihedral_angle_4_deg14.179
r_dihedral_angle_1_deg5.846
r_angle_refined_deg1.265
r_scangle_it1.256
r_angle_other_deg0.923
r_scbond_it0.793
r_mcangle_it0.699
r_mcbond_it0.423
r_symmetry_vdw_other0.229
r_nbd_refined0.221
r_nbd_other0.191
r_nbtor_refined0.187
r_xyhbond_nbd_refined0.178
r_symmetry_vdw_refined0.141
r_nbtor_other0.088
r_chiral_restr0.073
r_bond_refined_d0.012
r_gen_planes_refined0.004
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_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3686
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing