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Crystal structure of the nickel-activated two-domain iron-dependent regulator (IdeR)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FX7 PDB entry 1FX7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.2 298 0.6 M Na/K phosphate pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.25 45.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.954 α = 110.18 b = 44.743 β = 96.57 c = 49.641 γ = 108.29
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 2003-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 1.03320 APS 19-ID
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 1.95 50 91.8 0.06 12.6 20610
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) 1.95 2.02 58.1 0.173 1293
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 1FX7 1.955 45.13 20606 1058 91.51 0.178 0.176 0.1761 0.211 0.2106 RANDOM 28.607
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] 2.04 0.1 -0.6 -1.04 -1.29 -1.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.51 r_dihedral_angle_4_deg 23.683 r_dihedral_angle_3_deg 16.53 r_dihedral_angle_1_deg 5.046 r_scangle_it 3.688 r_scbond_it 2.651 r_mcangle_it 2.629 r_mcbond_it 1.695 r_angle_refined_deg 1.282 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.51 r_dihedral_angle_4_deg 23.683 r_dihedral_angle_3_deg 16.53 r_dihedral_angle_1_deg 5.046 r_scangle_it 3.688 r_scbond_it 2.651 r_mcangle_it 2.629 r_mcbond_it 1.695 r_angle_refined_deg 1.282 r_nbtor_refined 0.315 r_symmetry_vdw_refined 0.284 r_nbd_refined 0.234 r_xyhbond_nbd_refined 0.209 r_symmetry_hbond_refined 0.174 r_chiral_restr 0.097 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_metal_ion_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2359 Nucleic Acid Atoms Solvent Atoms 148 Heterogen Atoms 14
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection