X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6C1Ypdb entry 6c1y

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.529150% precipitant mix 4, 0.1M buffer system 1, 0.06M divalents (morpheus A4)
Crystal Properties
Matthews coefficientSolvent content
1.8734.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.47α = 90
b = 51.976β = 90
c = 66.304γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2018-09-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.10.97741ALS5.0.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.640.9199.80.060.0650.026117.56.118969
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6397.31.8352.0920.9820.3664.1891

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-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 6c1y1.6540.915648177399.960.22890.22590.255229.887
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]
0.67-1.751.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.027
r_dihedral_angle_4_deg24.813
r_dihedral_angle_3_deg13.015
r_dihedral_angle_1_deg6.407
r_angle_refined_deg1.743
r_mcangle_it1.649
r_angle_other_deg1.524
r_mcbond_other1.037
r_mcbond_it1.036
r_chiral_restr0.077
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.027
r_dihedral_angle_4_deg24.813
r_dihedral_angle_3_deg13.015
r_dihedral_angle_1_deg6.407
r_angle_refined_deg1.743
r_mcangle_it1.649
r_angle_other_deg1.524
r_mcbond_other1.037
r_mcbond_it1.036
r_chiral_restr0.077
r_gen_planes_refined0.018
r_bond_refined_d0.011
r_gen_planes_other0.008
r_bond_other_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms585
Nucleic Acid Atoms487
Solvent Atoms56
Heterogen Atoms18

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing