7HRG | pdb_00007hrg

PanDDA analysis group deposition -- Crystal Structure of FatA in complex with Z104474062


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
2.3647.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.595α = 90
b = 99.614β = 90
c = 127.835γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 9M2023-09-11SINGLE 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
11.9278.5999.60.1760.1830.050.9988.413.648653
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)
11.921.9697.81.0761.1170.30.93813.8

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 REPLACEMENTTHROUGHOUT1.9278.5844212225395.010.32510.322770.33020.370080.3699RANDOM53.211
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]
0.41-0.03-0.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.336
r_dihedral_angle_3_deg17.347
r_dihedral_angle_4_deg16.204
r_long_range_B_refined7.475
r_long_range_B_other7.446
r_dihedral_angle_1_deg6.113
r_scangle_other3.774
r_mcangle_it3.663
r_mcangle_other3.663
r_scbond_it1.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.336
r_dihedral_angle_3_deg17.347
r_dihedral_angle_4_deg16.204
r_long_range_B_refined7.475
r_long_range_B_other7.446
r_dihedral_angle_1_deg6.113
r_scangle_other3.774
r_mcangle_it3.663
r_mcangle_other3.663
r_scbond_it1.71
r_scbond_other1.705
r_mcbond_other1.647
r_mcbond_it1.631
r_angle_refined_deg1.304
r_angle_other_deg1.088
r_chiral_restr0.049
r_bond_refined_d0.004
r_gen_planes_refined0.004
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 Atoms4302
Nucleic Acid Atoms
Solvent Atoms130
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
REFMAC5refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction