7HQR | pdb_00007hqr

PanDDA analysis group deposition -- Crystal Structure of FatA in complex with Z56946871


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherin-house model

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.852930.1M MES pH 6.85, 1.6M Ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.3647.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.49α = 90
b = 99.472β = 90
c = 128.503γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 9M2023-05-16SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.92124DiamondI04-1

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
11.7770.3699.80.2820.2930.0790.9964.413.661983
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)
11.771.8196.64.554.7251.2670.39513.7

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 REPLACEMENTTHROUGHOUT1.7770.4454038275891.440.306340.303310.30260.365410.3519RANDOM46.344
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]
-2.26-0.662.92
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.685
r_dihedral_angle_4_deg20.488
r_dihedral_angle_3_deg18.055
r_long_range_B_refined15.862
r_long_range_B_other15.666
r_dihedral_angle_1_deg7.163
r_scangle_other4.698
r_mcangle_it4.553
r_mcangle_other4.553
r_scbond_other2.437
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.685
r_dihedral_angle_4_deg20.488
r_dihedral_angle_3_deg18.055
r_long_range_B_refined15.862
r_long_range_B_other15.666
r_dihedral_angle_1_deg7.163
r_scangle_other4.698
r_mcangle_it4.553
r_mcangle_other4.553
r_scbond_other2.437
r_scbond_it2.414
r_mcbond_other2.348
r_mcbond_it2.091
r_angle_refined_deg1.462
r_angle_other_deg1.147
r_chiral_restr0.061
r_bond_refined_d0.006
r_gen_planes_refined0.006
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4266
Nucleic Acid Atoms
Solvent Atoms421
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction