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Crystal structure of cytoplasmic metal binding domain with iron ions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6IU5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 21-23% PEG600, 0.1 M HEPES pH7.0 and 0.001-0.003 M zinc cloride
Crystal Properties Matthews coefficient Solvent content 2.81 56.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.321 α = 90 b = 85.321 β = 90 c = 97.573 γ = 120
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 PILATUS3 6M 2017-10-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.740 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 3 42.6607 99.9937 0.2096 0.2342 0.1035 0.9848 5.9655 5.139 15910
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 3 3.1073 99.9369 3.3153 0.0987 4.9565
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 6IU5 3 42.66 15192 718 99.95 0.1947 0.1916 0.1804 0.2649 0.2542 RANDOM 94.125
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] -9.68 -9.68 19.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.846 r_dihedral_angle_4_deg 23.993 r_dihedral_angle_3_deg 18.043 r_dihedral_angle_1_deg 5.847 r_angle_refined_deg 1.463 r_angle_other_deg 1.228 r_chiral_restr 0.068 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.846 r_dihedral_angle_4_deg 23.993 r_dihedral_angle_3_deg 18.043 r_dihedral_angle_1_deg 5.847 r_angle_refined_deg 1.463 r_angle_other_deg 1.228 r_chiral_restr 0.068 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4716 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing