7HSJ | pdb_00007hsj

PanDDA analysis group deposition -- Crystal Structure of FatA in complex with Z1639162606


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 = 99.549α = 90
b = 99.565β = 90
c = 128.3γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 9M2023-09-12SINGLE 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
11.8778.6899.50.1910.1990.0540.9988.913.752352
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.871.9292.90.44613.7

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 REPLACEMENTTHROUGHOUT1.8778.6648487243696.690.264590.261660.26580.320750.3141RANDOM53.836
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]
-0.84-0.91.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.258
r_dihedral_angle_4_deg18.707
r_dihedral_angle_3_deg17.738
r_long_range_B_refined15.591
r_long_range_B_other15.525
r_dihedral_angle_1_deg6.884
r_scangle_other6.089
r_mcangle_it5.421
r_mcangle_other5.421
r_scbond_other3.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.258
r_dihedral_angle_4_deg18.707
r_dihedral_angle_3_deg17.738
r_long_range_B_refined15.591
r_long_range_B_other15.525
r_dihedral_angle_1_deg6.884
r_scangle_other6.089
r_mcangle_it5.421
r_mcangle_other5.421
r_scbond_other3.26
r_scbond_it3.241
r_mcbond_other2.853
r_mcbond_it2.755
r_angle_refined_deg1.553
r_angle_other_deg1.185
r_chiral_restr0.065
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.001
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 Atoms4272
Nucleic Acid Atoms
Solvent Atoms218
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
REFMAC5refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction