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Detection of cobalt in previously unassigned human SENP1 structure
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IYC PDB ENTRY 2IYC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP CRYSTALLIZATION WAS PERFORMED USING A SITTING-DROP VAPOUR-DIFFUSION METHOD. CRYSTALS APPEARED FROM EQUAL VOLUMES OF PROTEIN SOLUTION (20 MG/ML IN 20 MM TRIS/HCL, PH 8.0, AND 50 MM NACL) AND RESERVOIR SOLUTION CONTAINING 100 MM COCL2, 0.1M MES, PH 6.5, AND 1.8 M (NH4)2SO4.
Crystal Properties Matthews coefficient Solvent content 2.74 55.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.981 α = 90 b = 71.981 β = 90 c = 200.64 γ = 120
Symmetry Space Group P 31 2 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 CCD ADSC CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 2.45 45.6 100 0.1 19 8.8 21832
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 2.45 2.51 100 0.43 3
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 2IYC 2.45 45.6 21829 1136 100 0.241 0.237 0.2395 0.317 0.2348 RANDOM 51.36
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] -0.02 -0.01 -0.02 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.532 r_dihedral_angle_3_deg 20.308 r_dihedral_angle_4_deg 14.202 r_scangle_it 7.856 r_dihedral_angle_1_deg 6.304 r_scbond_it 5.727 r_mcangle_it 3.716 r_mcbond_it 2.07 r_angle_refined_deg 1.525 r_chiral_restr 0.107
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.532 r_dihedral_angle_3_deg 20.308 r_dihedral_angle_4_deg 14.202 r_scangle_it 7.856 r_dihedral_angle_1_deg 6.304 r_scbond_it 5.727 r_mcangle_it 3.716 r_mcbond_it 2.07 r_angle_refined_deg 1.525 r_chiral_restr 0.107 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3705 Nucleic Acid Atoms Solvent Atoms 61 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing