9JWX | pdb_00009jwx

NifS soaked with(2R,3R)-3-ethoxycarbonylaziridine-2-carboxylic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5WT2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529385 mM HEPES/NaOH, 17%(w/v) PEG4000, 15%(v/v) glycerol, 8.5% (v/v) isopropanol
Crystal Properties
Matthews coefficientSolvent content
4.0269.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.18α = 90
b = 103.18β = 90
c = 133.35γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-12-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A0.98Photon FactoryBL-17A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.85099.90.0940.99919.5812.918331
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.999.90.9270.9623.5713.8

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 REPLACEMENTTHROUGHOUT5WT22.848.111741291799.920.20530.203250.20550.242850.2455RANDOM99.285
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]
-3.17-3.176.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.201
r_long_range_B_refined14.795
r_dihedral_angle_2_deg8.541
r_mcangle_it7.889
r_dihedral_angle_1_deg7.208
r_scbond_it5.548
r_mcbond_it4.949
r_angle_refined_deg2.058
r_chiral_restr0.167
r_gen_planes_refined0.009
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.201
r_long_range_B_refined14.795
r_dihedral_angle_2_deg8.541
r_mcangle_it7.889
r_dihedral_angle_1_deg7.208
r_scbond_it5.548
r_mcbond_it4.949
r_angle_refined_deg2.058
r_chiral_restr0.167
r_gen_planes_refined0.009
r_bond_refined_d0.008
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_4_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2817
Nucleic Acid Atoms
Solvent Atoms3
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing