4AIP

The FrpB iron transporter from Neisseria meningitidis (F3-3 variant)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3FHHPDB ENTRY 3FHH

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
160.6% (W/V) HEXYL-B-D-MALTOSIDE, 20 MM NA L-GLUTAMATE, 20 MM D, L-ALANINE, 20 MM GLYCINE, 20 MM LYSINE (RACEMIC), 20 MM SERINE (RACEMIC), 29 MM IMIDAZOLE, 11.6% (V/V) MPD, 11.6% (W/V) PEG 1000, 11.6% (W/V) PEG 3350 AND 71 MM MES (PH 6.0)
Crystal Properties
Matthews coefficientSolvent content
2.653

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.32α = 90
b = 104.62β = 90
c = 269.1γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS2011-04-18MSINGLE 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
12.413490.70.1110.23.8862352
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)
12.42.4683.10.382.32.2

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3FHH2.4134.5581658430190.440.244560.241830.29639RANDOM22.534
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]
0.16-0.40.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.138
r_dihedral_angle_4_deg22.848
r_dihedral_angle_3_deg20.304
r_dihedral_angle_1_deg7.671
r_scangle_it5.707
r_scbond_it3.765
r_mcangle_it2.852
r_angle_refined_deg2.136
r_mcbond_it1.529
r_chiral_restr0.143
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.138
r_dihedral_angle_4_deg22.848
r_dihedral_angle_3_deg20.304
r_dihedral_angle_1_deg7.671
r_scangle_it5.707
r_scbond_it3.765
r_mcangle_it2.852
r_angle_refined_deg2.136
r_mcbond_it1.529
r_chiral_restr0.143
r_bond_refined_d0.024
r_gen_planes_refined0.009
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 Atoms15599
Nucleic Acid Atoms
Solvent Atoms328
Heterogen Atoms58

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling