9JX7 | pdb_00009jx7

SufS in complex with (2R,3R)-3-ethoxycarbonylaziridine-2-carboxylic acid


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72930.1 M Tris-HCl, 50 mM Lithium sulfate, 50% (v/v) PEG200
Crystal Properties
Matthews coefficientSolvent content
3.4864.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.97α = 90
b = 92.97β = 90
c = 129.9γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2022-09-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1SLSX06SA

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
11.85099.50.0620.064124.7918.160716
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)
11.81.90.870.9210.782

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6KFY1.846.4957496302799.650.160720.159440.17190.18560.1945RANDOM35.921
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]
0.060.030.06-0.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.493
r_dihedral_angle_2_deg9.024
r_long_range_B_refined7.526
r_long_range_B_other7.44
r_dihedral_angle_1_deg6.355
r_scangle_other5.79
r_scbond_other4.051
r_scbond_it4.049
r_mcangle_other3.185
r_mcangle_it3.182
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.493
r_dihedral_angle_2_deg9.024
r_long_range_B_refined7.526
r_long_range_B_other7.44
r_dihedral_angle_1_deg6.355
r_scangle_other5.79
r_scbond_other4.051
r_scbond_it4.049
r_mcangle_other3.185
r_mcangle_it3.182
r_mcbond_it2.484
r_mcbond_other2.477
r_angle_refined_deg1.933
r_angle_other_deg0.7
r_chiral_restr0.107
r_bond_refined_d0.013
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3162
Nucleic Acid Atoms
Solvent Atoms312
Heterogen Atoms51

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing