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The FrpB iron transporter from Neisseria meningitidis (F5-1 variant)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4AIP PDB ENTRY 4AIP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 30 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 coefficient Solvent content 3.4 64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 175.98 α = 90 b = 78.69 β = 97.22 c = 73.43 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTIS PILATUS 2011-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.6 36 97.4 0.06 12.7 2.6 29989 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.67 98.9 0.52 2.2 2.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (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 Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 4AIP 2.6 36.42 28422 1506 97.25 0.22918 0.22654 0.2227 0.27749 0.2758 RANDOM 48.868
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 -2.92 0.34 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.69 r_dihedral_angle_4_deg 21.367 r_dihedral_angle_3_deg 19.909 r_dihedral_angle_1_deg 8.376 r_scangle_it 5.386 r_scbond_it 3.257 r_angle_refined_deg 2.16 r_mcangle_it 2.019 r_mcbond_it 1.039 r_chiral_restr 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.69 r_dihedral_angle_4_deg 21.367 r_dihedral_angle_3_deg 19.909 r_dihedral_angle_1_deg 8.376 r_scangle_it 5.386 r_scbond_it 3.257 r_angle_refined_deg 2.16 r_mcangle_it 2.019 r_mcbond_it 1.039 r_chiral_restr 0.15 r_bond_refined_d 0.024 r_gen_planes_refined 0.002 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 Atoms Number Protein Atoms 5168 Nucleic Acid Atoms Solvent Atoms 44 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing