X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.929330% w/v PEG3350, 0.2 M AmCl
Crystal Properties
Matthews coefficientSolvent content
2.1743.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.525α = 90
b = 88.945β = 91.61
c = 41.7γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2015-02-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.979DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.3841.5980.1370.9937.46.560739
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)
11.381.4282.50.8541.44.7

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 REPLACEMENTTHROUGHOUT1KEX1.644.4737803193599.660.147930.145910.18705RANDOM13.416
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]
-0.3-0.030.020.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.214
r_dihedral_angle_4_deg16.392
r_dihedral_angle_3_deg12.04
r_dihedral_angle_1_deg7.087
r_long_range_B_refined6.213
r_long_range_B_other5.883
r_scangle_other3.9
r_scbond_it2.56
r_scbond_other2.559
r_angle_refined_deg2.117
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.214
r_dihedral_angle_4_deg16.392
r_dihedral_angle_3_deg12.04
r_dihedral_angle_1_deg7.087
r_long_range_B_refined6.213
r_long_range_B_other5.883
r_scangle_other3.9
r_scbond_it2.56
r_scbond_other2.559
r_angle_refined_deg2.117
r_mcangle_it1.963
r_mcangle_other1.963
r_angle_other_deg1.366
r_mcbond_it1.36
r_mcbond_other1.352
r_chiral_restr0.131
r_bond_refined_d0.024
r_gen_planes_refined0.014
r_bond_other_d0.007
r_gen_planes_other0.006
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 Atoms2501
Nucleic Acid Atoms
Solvent Atoms479
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing