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Crystal structure of cytoplasmic metal binding domain with zinc ions
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 56.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.942 α = 90 b = 84.942 β = 90 c = 98.19 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 2017-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.282 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 2.25 42.4712 99.7978 0.1445 0.1654 0.0797 0.9902 5.5282 4.1795 37519
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 2.25 2.3304 99.096 1.19 0.3859 3.7116
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2.25 42.51 35762 1757 99.75 0.19993 0.19757 0.2093 0.25002 0.2584 RANDOM 54.551
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] -0.46 -0.23 -0.46 1.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.585 r_dihedral_angle_4_deg 23.656 r_dihedral_angle_3_deg 18.274 r_scangle_other 8.084 r_mcangle_it 6.742 r_mcangle_other 6.741 r_scbond_it 5.618 r_scbond_other 5.617 r_dihedral_angle_1_deg 5.458 r_mcbond_it 4.855
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.585 r_dihedral_angle_4_deg 23.656 r_dihedral_angle_3_deg 18.274 r_scangle_other 8.084 r_mcangle_it 6.742 r_mcangle_other 6.741 r_scbond_it 5.618 r_scbond_other 5.617 r_dihedral_angle_1_deg 5.458 r_mcbond_it 4.855 r_mcbond_other 4.855 r_angle_refined_deg 1.589 r_angle_other_deg 1.325 r_chiral_restr 0.086 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4716 Nucleic Acid Atoms Solvent Atoms 214 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction AutoSol phasing