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Crystal structure of cytoplasmic metal binding domain with cobalt 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 2.85 56.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.503 α = 90 b = 85.503 β = 90 c = 98.355 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 2017-07-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.6050 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 2.7 19.72 99.7 0.131 0.138 0.042 0.997 11.2 10.4 22053
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.83 100 0.74 0.778 0.239 0.761 10.5
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 (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 2.7 19.72 21040 986 99.74 0.1608 0.1584 0.1652 0.2147 0.2149 RANDOM 66.018
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] 1.53 1.53 -3.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.229 r_dihedral_angle_4_deg 22.973 r_dihedral_angle_3_deg 18.956 r_dihedral_angle_1_deg 6.349 r_angle_refined_deg 1.575 r_angle_other_deg 1.22 r_chiral_restr 0.074 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.229 r_dihedral_angle_4_deg 22.973 r_dihedral_angle_3_deg 18.956 r_dihedral_angle_1_deg 6.349 r_angle_refined_deg 1.575 r_angle_other_deg 1.22 r_chiral_restr 0.074 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4716 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing