X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE7.52916-10 mg/mL of protein in 50mM Sodium acteate, 150mM NaCl pH 5 mixed with 100 mM MgCl2, 100 mM HEPES pH 7.5, 16% PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.4750.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.79α = 90
b = 120.27β = 90
c = 196.01γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2019-08-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.8SLSX10SA

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
11.9949.0599.20.2270.9717.56.913808928.2
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)
11.992.0297.11.020.4982.15

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 REPLACEMENTTHROUGHOUTSFX structure of ferric DtpB1.9949.05131265682499.040.17820.17610.2179RANDOM30.279
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]
-0.10.040.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.472
r_dihedral_angle_4_deg17.602
r_dihedral_angle_3_deg12.44
r_dihedral_angle_1_deg7.322
r_angle_refined_deg1.584
r_angle_other_deg1.35
r_chiral_restr0.07
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_gen_planes_other0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.472
r_dihedral_angle_4_deg17.602
r_dihedral_angle_3_deg12.44
r_dihedral_angle_1_deg7.322
r_angle_refined_deg1.584
r_angle_other_deg1.35
r_chiral_restr0.07
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_gen_planes_other0.006
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13912
Nucleic Acid Atoms
Solvent Atoms1142
Heterogen Atoms375

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
REFMACphasing