X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3R38 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.42932.5mM UNAG and 2.5mM fosfomycin in the buffer containing 0.22 M Potassium sodium tartrate tetrahydrate, 26% w/v Polyethylene glycol 3,350, pH 7.4
Crystal Properties
Matthews coefficientSolvent content
3.0259.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.03α = 115.06
b = 96.81β = 99.15
c = 96.821γ = 103.88
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2018-08-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

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
11.6546.9997.270.1010.11670.9959.09425721716.56
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)
11.651.70995.680.82750.9560.6351.944

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 REPLACEMENTTHROUGHOUT3R381.6547.822445121270797.280.117880.115930.15752RANDOM18.24
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]
0.79-0.090.1-0.02-0.790.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.13
r_dihedral_angle_4_deg17.865
r_dihedral_angle_3_deg11.861
r_dihedral_angle_1_deg6.146
r_long_range_B_refined4.419
r_long_range_B_other4.06
r_rigid_bond_restr3.77
r_scangle_other3.546
r_scbond_it2.89
r_scbond_other2.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.13
r_dihedral_angle_4_deg17.865
r_dihedral_angle_3_deg11.861
r_dihedral_angle_1_deg6.146
r_long_range_B_refined4.419
r_long_range_B_other4.06
r_rigid_bond_restr3.77
r_scangle_other3.546
r_scbond_it2.89
r_scbond_other2.89
r_mcangle_other2.637
r_mcangle_it2.636
r_mcbond_it2.018
r_mcbond_other2.014
r_angle_refined_deg1.705
r_angle_other_deg1.513
r_chiral_restr0.101
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
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_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12721
Nucleic Acid Atoms
Solvent Atoms1596
Heterogen Atoms205

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing