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Crystal structure of Domain Related to Iron (DRI) from cyanobacteria
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5BNC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 25% PEG3350, 100 mM Bis-Tris, pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.84 56.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.716 α = 90 b = 87.23 β = 94.981 c = 57.241 γ = 90
Symmetry Space Group P 1 21 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 DECTRIS EIGER X 16M 2019-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.9793 NSLS-II 17-ID-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.35 29.5 99 0.055 0.99 15 5.3 20972 56.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.41 87.8 0.736 0.76 1.9 5
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 5BNC 2.35 29.5 20954 1027 98.989 0.199 0.197 0.2022 0.2474 0.2535 61.989
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] -0.376 2.54 -3.183 3.069
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.667 r_dihedral_angle_3_deg 21.944 r_dihedral_angle_4_deg 21.056 r_lrange_it 12.529 r_lrange_other 12.529 r_scangle_it 8.698 r_scangle_other 8.696 r_mcangle_it 8.181 r_mcangle_other 8.178 r_dihedral_angle_1_deg 6.696
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.667 r_dihedral_angle_3_deg 21.944 r_dihedral_angle_4_deg 21.056 r_lrange_it 12.529 r_lrange_other 12.529 r_scangle_it 8.698 r_scangle_other 8.696 r_mcangle_it 8.181 r_mcangle_other 8.178 r_dihedral_angle_1_deg 6.696 r_scbond_it 5.644 r_scbond_other 5.642 r_mcbond_other 5.427 r_mcbond_it 5.425 r_angle_refined_deg 1.545 r_angle_other_deg 1.341 r_nbd_other 0.24 r_symmetry_nbd_refined 0.224 r_nbd_refined 0.21 r_symmetry_nbd_other 0.203 r_nbtor_refined 0.161 r_symmetry_xyhbond_nbd_refined 0.148 r_xyhbond_nbd_refined 0.138 r_symmetry_xyhbond_nbd_other 0.113 r_symmetry_nbtor_other 0.089 r_metal_ion_refined 0.085 r_chiral_restr 0.059 r_symmetry_metal_ion_refined 0.011 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3096 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing