9JFC | pdb_00009jfc

Crystal structure of Pseudomonas aeruginosa SuhB complexed with Gallic acid in monoclinic space group


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8WDQ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP298PEG 3350, Sodium acetate trihydrate
Crystal Properties
Matthews coefficientSolvent content
2.1442.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.173α = 90
b = 90.603β = 90
c = 89.953γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2024-06-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONRRCAT INDUS-2 BEAMLINE PX-BL210.97893RRCAT INDUS-2PX-BL21

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.245.399.60.0890.1040.0540.99510.53.850522
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.3299.90.2820.3290.1680.9283.8

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.244.9847996250599.520.184750.182350.17060.233590.2193RANDOM24.758
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]
22.611.35-11.4-11.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.346
r_dihedral_angle_4_deg19.817
r_dihedral_angle_3_deg18.91
r_dihedral_angle_1_deg7.611
r_long_range_B_refined5.879
r_long_range_B_other5.834
r_scangle_other2.639
r_mcangle_it2.583
r_mcangle_other2.583
r_angle_refined_deg1.909
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.346
r_dihedral_angle_4_deg19.817
r_dihedral_angle_3_deg18.91
r_dihedral_angle_1_deg7.611
r_long_range_B_refined5.879
r_long_range_B_other5.834
r_scangle_other2.639
r_mcangle_it2.583
r_mcangle_other2.583
r_angle_refined_deg1.909
r_scbond_it1.721
r_scbond_other1.721
r_mcbond_it1.663
r_mcbond_other1.663
r_angle_other_deg1.447
r_chiral_restr0.091
r_bond_refined_d0.015
r_gen_planes_refined0.011
r_bond_other_d0.002
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8288
Nucleic Acid Atoms
Solvent Atoms333
Heterogen Atoms94

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SCALAdata scaling
XDSdata reduction
PHASERphasing