X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3KLQ3KLQ and 1ANF
experimental modelPDB 1ANF3KLQ and 1ANF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529112.5% PEG 1000, 10% PEG 3350, 12.5% MPD, 0.1M MES/imidazole pH 6.5, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium L-tartrate, 0.02 M sodium oxamate
Crystal Properties
Matthews coefficientSolvent content
2.6854.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 180.359α = 90
b = 192.093β = 90
c = 68.204γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2013-08-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.9537Australian SynchrotronMX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
1219.5798.50.99710.37.478932
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.1197.80.5251.67.4

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 REPLACEMENTTHROUGHOUT3KLQ and 1ANF219.5774971396098.320.196020.194180.22991RANDOM39.681
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]
-0.110.28-0.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.319
r_dihedral_angle_4_deg13.621
r_dihedral_angle_3_deg13.165
r_long_range_B_refined6.479
r_long_range_B_other6.449
r_dihedral_angle_1_deg5.818
r_scangle_other4.903
r_mcangle_it3.545
r_mcangle_other3.544
r_scbond_it3.064
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.319
r_dihedral_angle_4_deg13.621
r_dihedral_angle_3_deg13.165
r_long_range_B_refined6.479
r_long_range_B_other6.449
r_dihedral_angle_1_deg5.818
r_scangle_other4.903
r_mcangle_it3.545
r_mcangle_other3.544
r_scbond_it3.064
r_scbond_other3.06
r_mcbond_it2.332
r_mcbond_other2.332
r_angle_refined_deg1.393
r_angle_other_deg0.769
r_chiral_restr0.078
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6502
Nucleic Acid Atoms
Solvent Atoms277
Heterogen Atoms80

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing