6Z33

Crystal structure of the ferric enterobactin receptor (PfeA) in complex with BCV


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6Q5E 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION294PEG 8000 ADA Magnesium acetate
Crystal Properties
Matthews coefficientSolvent content
3.4664.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.962α = 90
b = 157.358β = 90
c = 78.077γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2020-03-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97625DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.71178.679830.062116.97.524453
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)
12.7112.8580.555

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6q5E2.71178.67924453117182.9840.2270.22580.2515101.994
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]
-0.445-0.9451.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.687
r_dihedral_angle_4_deg17.275
r_dihedral_angle_3_deg17.113
r_lrange_it12.081
r_lrange_other12.08
r_dihedral_angle_1_deg9.639
r_scangle_it9.498
r_scangle_other9.497
r_mcangle_it9.076
r_mcangle_other9.075
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.687
r_dihedral_angle_4_deg17.275
r_dihedral_angle_3_deg17.113
r_lrange_it12.081
r_lrange_other12.08
r_dihedral_angle_1_deg9.639
r_scangle_it9.498
r_scangle_other9.497
r_mcangle_it9.076
r_mcangle_other9.075
r_scbond_it7.134
r_scbond_other7.122
r_mcbond_other6.649
r_mcbond_it6.648
r_angle_refined_deg1.255
r_angle_other_deg1.073
r_nbd_other0.301
r_symmetry_nbd_refined0.237
r_nbd_refined0.208
r_symmetry_nbd_other0.207
r_xyhbond_nbd_refined0.168
r_nbtor_refined0.166
r_symmetry_nbtor_other0.074
r_chiral_restr0.049
r_symmetry_xyhbond_nbd_other0.044
r_gen_planes_refined0.022
r_ext_dist_refined_d0.02
r_gen_planes_other0.014
r_bond_refined_d0.009
r_bond_other_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5370
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing