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Crystal structure of the Vibrio cholerae ferric uptake regulator (Fur) reveals structural rearrangement of the DNA-binding domains
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MZB PDB ENTRIES 1MZB,2FU4 experimental model PDB 2FU4 PDB ENTRIES 1MZB,2FU4
Crystallization Crystal Properties Matthews coefficient Solvent content 2.47 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.88 α = 90 b = 88.88 β = 90 c = 85.07 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RIGAKU SATURN 944 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF
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 18 100 0.13 16.6 8.6 10961
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 2.74 100 0.6 3.3 8.6
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 ENTRIES 1MZB,2FU4 2.6 62.87 10383 522 99.3 0.218 0.216 0.2145 0.259 0.2571 RANDOM
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.475 r_dihedral_angle_4_deg 23.05 r_dihedral_angle_3_deg 16.691 r_dihedral_angle_1_deg 5.467 r_scangle_it 2.383 r_scbond_it 1.455 r_angle_refined_deg 1.215 r_mcangle_it 1.19 r_mcbond_it 0.674 r_xyhbond_nbd_refined 0.321
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.475 r_dihedral_angle_4_deg 23.05 r_dihedral_angle_3_deg 16.691 r_dihedral_angle_1_deg 5.467 r_scangle_it 2.383 r_scbond_it 1.455 r_angle_refined_deg 1.215 r_mcangle_it 1.19 r_mcbond_it 0.674 r_xyhbond_nbd_refined 0.321 r_nbtor_refined 0.299 r_symmetry_vdw_refined 0.22 r_nbd_refined 0.199 r_symmetry_hbond_refined 0.14 r_chiral_restr 0.069 r_metal_ion_refined 0.064 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other 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 2100 Nucleic Acid Atoms Solvent Atoms 79 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing