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DUF4198 protein from Ideonella sakaiensis with Ni bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 Na malonate, HEPES, Jeffamine D2001
Crystal Properties Matthews coefficient Solvent content 2.24 45.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.532 α = 81.421 b = 47.468 β = 81.502 c = 49.452 γ = 83.599
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 EIGER2 XE 16M 2021-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 1.44 48.46 64.1 0.033 0.046 0.033 0.998 18.2 3.3 44708
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) 1.44 1.47 4.1 0.157 0.221 0.157 0.909 1.9 1.2
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.44 48.46 44705 2199 64.128 0.132 0.1296 0.1296 0.1824 0.1824 15.519
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] 0.259 -0.03 1.472 -0.845 -0.886 0.725
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.561 r_dihedral_angle_3_deg 11.655 r_lrange_it 11.628 r_dihedral_angle_2_deg 9.515 r_scangle_it 6.508 r_dihedral_angle_1_deg 6.069 r_mcangle_it 4.696 r_scbond_it 4.558 r_rigid_bond_restr 4.193 r_mcbond_it 3.196
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.561 r_dihedral_angle_3_deg 11.655 r_lrange_it 11.628 r_dihedral_angle_2_deg 9.515 r_scangle_it 6.508 r_dihedral_angle_1_deg 6.069 r_mcangle_it 4.696 r_scbond_it 4.558 r_rigid_bond_restr 4.193 r_mcbond_it 3.196 r_angle_refined_deg 1.751 r_nbtor_refined 0.311 r_symmetry_nbd_refined 0.215 r_nbd_refined 0.198 r_symmetry_xyhbond_nbd_refined 0.174 r_xyhbond_nbd_refined 0.165 r_chiral_restr 0.123 r_ncsr_local_group_1 0.117 r_bond_refined_d 0.009 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3112 Nucleic Acid Atoms Solvent Atoms 480 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling REFMAC phasing