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De novo designed two-domain di-Zn(II) and porphyrin-binding protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other Designed model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 22% PEG 4000
100 mM MgCl2
100 mM Hepes pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.41 49.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 172.478 α = 90 b = 27.825 β = 117.16 c = 188.494 γ = 90
Symmetry Space Group C 1 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 PIXEL DECTRIS PILATUS3 6M 2018-01-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.11583 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 3.5 86.24 99.63 0.1552 0.06219 0.997 6.49 6.2 10708
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.5 3.625 100 2.184 2.379 0.322 0.8 6.4
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 Designed model 3.5 86.24 10202 503 99.76 0.26167 0.26059 0.2756 0.28319 0.3033 RANDOM
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] 2.7 -4.58 2.29 -0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.814 r_dihedral_angle_4_deg 21.449 r_dihedral_angle_3_deg 19.193 r_long_range_B_refined 6.321 r_long_range_B_other 6.321 r_dihedral_angle_1_deg 5.387 r_mcangle_it 2.21 r_mcangle_other 2.21 r_scangle_other 1.939 r_mcbond_it 1.231
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.814 r_dihedral_angle_4_deg 21.449 r_dihedral_angle_3_deg 19.193 r_long_range_B_refined 6.321 r_long_range_B_other 6.321 r_dihedral_angle_1_deg 5.387 r_mcangle_it 2.21 r_mcangle_other 2.21 r_scangle_other 1.939 r_mcbond_it 1.231 r_mcbond_other 1.231 r_scbond_it 1.027 r_scbond_other 1.027 r_angle_refined_deg 0.973 r_angle_other_deg 0.687 r_chiral_restr 0.038 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 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 5880 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms 200
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing