9D7C | pdb_00009d7c

OXA-58-NA-1-157 10 min complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4OH0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2890.2 M sodium acetate, 0.1 M Tris-HCl pH 8.5, 30% PEG4000
Crystal Properties
Matthews coefficientSolvent content
1.8734.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.01α = 90
b = 65.771β = 91.19
c = 193.101γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2024-06-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-20.9795SSRLBL12-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)Rpim 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
11.9454.4191.30.2050.080.9815.36.562529
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.941.980.640.5581.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT1.9454.4159268301091.110.219950.218460.22360.248710.2548RANDOM29.554
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]
-2.620.593.31-0.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg11.705
r_dihedral_angle_1_deg5.87
r_dihedral_angle_2_deg3.219
r_long_range_B_refined3.089
r_long_range_B_other3.063
r_scangle_other1.847
r_mcangle_it1.806
r_mcangle_other1.806
r_angle_refined_deg1.044
r_scbond_it1.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg11.705
r_dihedral_angle_1_deg5.87
r_dihedral_angle_2_deg3.219
r_long_range_B_refined3.089
r_long_range_B_other3.063
r_scangle_other1.847
r_mcangle_it1.806
r_mcangle_other1.806
r_angle_refined_deg1.044
r_scbond_it1.04
r_scbond_other1.04
r_mcbond_it1.03
r_mcbond_other1.03
r_angle_other_deg0.366
r_chiral_restr0.048
r_gen_planes_refined0.003
r_bond_refined_d0.002
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 Atoms7644
Nucleic Acid Atoms
Solvent Atoms208
Heterogen Atoms110

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing