X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5GGW 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.52890.2 M Lithium Sulfate, 30% PEG 8000, 0.1 M Sodium Acetate:Acetic Acid buffer
Crystal Properties
Matthews coefficientSolvent content
2.7655.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 127.929α = 90
b = 127.929β = 90
c = 93.02γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2018-10-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.9792APS19-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.647.6499.70.0630.0660.02113.19112960
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)
11.61.6395.20.610.7010.3370.6871.543.9

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 REPLACEMENTTHROUGHOUT5GGW1.647.64107309562099.610.13840.13750.1557RANDOM20.122
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]
0.030.020.03-0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.364
r_dihedral_angle_3_deg13.188
r_dihedral_angle_4_deg12.695
r_dihedral_angle_1_deg6.601
r_angle_refined_deg1.672
r_angle_other_deg1.497
r_chiral_restr0.089
r_bond_refined_d0.011
r_gen_planes_refined0.01
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.364
r_dihedral_angle_3_deg13.188
r_dihedral_angle_4_deg12.695
r_dihedral_angle_1_deg6.601
r_angle_refined_deg1.672
r_angle_other_deg1.497
r_chiral_restr0.089
r_bond_refined_d0.011
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5602
Nucleic Acid Atoms
Solvent Atoms631
Heterogen Atoms38

Software

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