X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4KMT 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2771.86 M ammonium sulfate, 8 mM CoCl2, 30 mM K/Na phosphate, pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.6954.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 136.127α = 90
b = 136.127β = 90
c = 175.956γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2015-07-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B1.03316APS23-ID-B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.8107.989913.998.976265
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.82.6630.244

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 REPLACEMENTTHROUGHOUT4KMT1.8107.972436381399.980.183150.181920.2068RANDOM37.237
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]
0.440.44-0.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.838
r_dihedral_angle_4_deg18.063
r_dihedral_angle_3_deg14.259
r_long_range_B_other10.143
r_long_range_B_refined10.14
r_scangle_other7.816
r_dihedral_angle_1_deg7.439
r_scbond_it5.724
r_scbond_other5.723
r_mcangle_it4.722
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.838
r_dihedral_angle_4_deg18.063
r_dihedral_angle_3_deg14.259
r_long_range_B_other10.143
r_long_range_B_refined10.14
r_scangle_other7.816
r_dihedral_angle_1_deg7.439
r_scbond_it5.724
r_scbond_other5.723
r_mcangle_it4.722
r_mcangle_other4.721
r_mcbond_it3.649
r_mcbond_other3.648
r_angle_refined_deg2.059
r_angle_other_deg1.136
r_chiral_restr0.139
r_bond_refined_d0.025
r_gen_planes_refined0.011
r_bond_other_d0.007
r_gen_planes_other0.002
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 Atoms5059
Nucleic Acid Atoms
Solvent Atoms560
Heterogen Atoms102

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata scaling
Cootmodel building
XDSdata processing