X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6Q2C 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72960.1 M sodium-cocydylate; 0.12 M Guanidine hydrochloride; 2% Jefframine M-600, pH 7.0
Crystal Properties
Matthews coefficientSolvent content
3.0259.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 117.98α = 90
b = 177.22β = 90
c = 181.52γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110PIXELDECTRIS PILATUS3 S 6Mmirrors2019-08-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.1159ALS8.3.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim 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
12.92127.131000.4010.4170.9947.1213.538326970.545
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.92399.94.6944.8760.2640.6413.607

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 REPLACEMENTTHROUGHOUT6Q2C2.92127.1379148404399.980.21290.2090.2905RANDOM79.017
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]
4.64-3.32-1.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.229
r_dihedral_angle_3_deg18.56
r_dihedral_angle_4_deg16.095
r_dihedral_angle_1_deg7.102
r_angle_refined_deg1.577
r_angle_other_deg1.02
r_chiral_restr0.088
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.229
r_dihedral_angle_3_deg18.56
r_dihedral_angle_4_deg16.095
r_dihedral_angle_1_deg7.102
r_angle_refined_deg1.577
r_angle_other_deg1.02
r_chiral_restr0.088
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms21135
Nucleic Acid Atoms
Solvent Atoms46
Heterogen Atoms420

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing