X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6S0T 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52891:1 of 28% PEG4000 (w/v), 0.5 M lithium sulfate, 0.1 M HEPES, 0.1 M sodium acetate and 15mg/ml protein in 0.05 M bis-tris methane, 0.15 M NaCl; soaked with 0.02 M neamine
Crystal Properties
Matthews coefficientSolvent content
5.3677.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.467α = 90
b = 185.25β = 94.68
c = 110.46γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9MBimorph K-B pair2018-07-27MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D0.97938APS21-ID-D

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
1348.5490.740.1260.9826.65.240424
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)
133.050.9470.661

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT6S0T348.5434821179390.740.201120.199730.22824RANDOM60.168
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]
1.46-0.360.22-1.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.501
r_dihedral_angle_4_deg16.412
r_dihedral_angle_3_deg13.403
r_long_range_B_other9.526
r_long_range_B_refined9.524
r_dihedral_angle_1_deg7.568
r_mcangle_it2.794
r_mcangle_other2.794
r_scangle_other2.752
r_scbond_it1.734
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.501
r_dihedral_angle_4_deg16.412
r_dihedral_angle_3_deg13.403
r_long_range_B_other9.526
r_long_range_B_refined9.524
r_dihedral_angle_1_deg7.568
r_mcangle_it2.794
r_mcangle_other2.794
r_scangle_other2.752
r_scbond_it1.734
r_scbond_other1.734
r_mcbond_it1.584
r_mcbond_other1.584
r_angle_refined_deg1.351
r_angle_other_deg1.337
r_chiral_restr0.058
r_gen_planes_other0.017
r_gen_planes_refined0.009
r_bond_refined_d0.007
r_bond_other_d0.004
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 Atoms13104
Nucleic Acid Atoms
Solvent Atoms145
Heterogen Atoms228

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing