X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3GPG 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.629121-24% PEG 400, 0.1 M sodium citrate pH5.6, 10% isopropanol
Crystal Properties
Matthews coefficientSolvent content
2.5351.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.068α = 90
b = 88.068β = 90
c = 83.779γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2017-08-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.6476.29990.05217.25.688999
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)
11.641.730.612.7

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 REPLACEMENTTHROUGHOUT3GPG1.6476.2784554442099.980.1890.18810.2063RANDOM26.62
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]
0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.045
r_dihedral_angle_4_deg17.001
r_dihedral_angle_3_deg13.652
r_dihedral_angle_1_deg6.135
r_angle_other_deg1.261
r_angle_refined_deg1.21
r_chiral_restr0.053
r_gen_planes_refined0.005
r_bond_refined_d0.004
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.045
r_dihedral_angle_4_deg17.001
r_dihedral_angle_3_deg13.652
r_dihedral_angle_1_deg6.135
r_angle_other_deg1.261
r_angle_refined_deg1.21
r_chiral_restr0.053
r_gen_planes_refined0.005
r_bond_refined_d0.004
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4906
Nucleic Acid Atoms
Solvent Atoms415
Heterogen Atoms144

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACTdata extraction