4AIQ | pdb_00004aiq

The FrpB iron transporter from Neisseria meningitidis (F5-1 variant)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4AIPPDB ENTRY 4AIP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.530 MM DI-ETHYLENE GLYCOL, 30 MM TRI-ETHYLENE GLYCOL, 30 MM TETRA-ETHYLENE GLYCOL, 30 MM PENTA-ETHYLENE GLYCOL, 45 MM IMIDAZOLE, 20% (W/V) PEGMME550, 10% (W/V) PEG 20000 AND 56 MM MES (PH 6.5)
Crystal Properties
Matthews coefficientSolvent content
3.464

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 175.98α = 90
b = 78.69β = 97.22
c = 73.43γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTIS PILATUS2011-10-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I24DiamondI24

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.63697.40.0612.72.6299892
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.6798.90.522.22.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUTPDB ENTRY 4AIP2.636.4228422150697.250.229180.226540.220.277490.28RANDOM48.868
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]
-0.92-2.920.34-0.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.69
r_dihedral_angle_4_deg21.367
r_dihedral_angle_3_deg19.909
r_dihedral_angle_1_deg8.376
r_scangle_it5.386
r_scbond_it3.257
r_angle_refined_deg2.16
r_mcangle_it2.019
r_mcbond_it1.039
r_chiral_restr0.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.69
r_dihedral_angle_4_deg21.367
r_dihedral_angle_3_deg19.909
r_dihedral_angle_1_deg8.376
r_scangle_it5.386
r_scbond_it3.257
r_angle_refined_deg2.16
r_mcangle_it2.019
r_mcbond_it1.039
r_chiral_restr0.15
r_bond_refined_d0.024
r_gen_planes_refined0.002
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5168
Nucleic Acid Atoms
Solvent Atoms44
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing