X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DVN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52770.2 M Ammonium acetate, 0.1 M Tris pH 8.5, 25% w/v PEG 3,350, 277 K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.7655.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 150.9α = 90
b = 62.3β = 105.5
c = 52.2γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPilatus2007-11-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.0001SLSX10SA

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
11.9339.94970.0686.43597334894-3-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.931.9895.50.4740.4744.36.4

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1DVN1.9339.94359733220217041000.18260.180720.21832RANDOM32.314
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]
-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.974
r_dihedral_angle_4_deg17.77
r_dihedral_angle_3_deg13.828
r_dihedral_angle_1_deg5.977
r_scangle_it3.227
r_scbond_it2.016
r_mcangle_it1.369
r_angle_refined_deg1.361
r_mcbond_it0.735
r_chiral_restr0.089
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.974
r_dihedral_angle_4_deg17.77
r_dihedral_angle_3_deg13.828
r_dihedral_angle_1_deg5.977
r_scangle_it3.227
r_scbond_it2.016
r_mcangle_it1.369
r_angle_refined_deg1.361
r_mcbond_it0.735
r_chiral_restr0.089
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2895
Nucleic Acid Atoms
Solvent Atoms227
Heterogen Atoms

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction