6US6

Artificial Iron Proteins: Modelling the Active Sites in Non-Heme Dioxygenases


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2QCB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP429526 mg/mL protein, 2.0 M ammonium sulfate, 0.1 M sodium acetate pH 4
Crystal Properties
Matthews coefficientSolvent content
2.3748.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.117α = 90
b = 58.117β = 90
c = 185.667γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray300CCDRAYONIX MX340-HS2018-12-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSLAC LCLS BEAMLINE MFX1.3017SLAC LCLSMFX

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1injection
Data Reduction
Diffraction IDFrames IndexedCrystal HitsTotal Frames
16011

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.523.2299.80.97727.54499.9826030
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5599.50.240.96713.24

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 REPLACEMENTTHROUGHOUT2QCB1.523.2224705132599.750.16820.16740.1821RANDOM21.843
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]
0.010.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.041
r_dihedral_angle_4_deg23.856
r_dihedral_angle_3_deg14.677
r_dihedral_angle_1_deg7.345
r_angle_other_deg2.543
r_angle_refined_deg1.996
r_chiral_restr0.089
r_bond_other_d0.038
r_gen_planes_other0.022
r_bond_refined_d0.015
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.041
r_dihedral_angle_4_deg23.856
r_dihedral_angle_3_deg14.677
r_dihedral_angle_1_deg7.345
r_angle_other_deg2.543
r_angle_refined_deg1.996
r_chiral_restr0.089
r_bond_other_d0.038
r_gen_planes_other0.022
r_bond_refined_d0.015
r_gen_planes_refined0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms935
Nucleic Acid Atoms
Solvent Atoms63
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
cctbx.xfeldata reduction
DIALSdata scaling
PHASERphasing