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De novo designed S-locus Protein 11 (SP11)-like protein (P212121 form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other Colabfold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 0.5M di-ammonium tartrate, 17.5% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.96 58.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.234 α = 90 b = 82.828 β = 90 c = 118.21 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS 6M 2023-05-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.000 SPring-8 BL45XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.09 48.16 99.9 0.19 0.999 24.5 27 46962 27.69
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.09 2.22 99.3 1.497 0.918 3.3
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 MOLECULAR REPLACEMENT THROUGHOUT 2.1 48.16 44357 2321 99.99 0.20197 0.20012 0.2067 0.23925 0.2451 RANDOM 58.905
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] -0.6 2.21 -1.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.489 r_dihedral_angle_2_deg 14.054 r_long_range_B_other 11.798 r_long_range_B_refined 11.776 r_scangle_other 9.939 r_mcangle_it 7.266 r_mcangle_other 7.265 r_scbond_it 6.753 r_scbond_other 6.753 r_dihedral_angle_1_deg 5.908
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.489 r_dihedral_angle_2_deg 14.054 r_long_range_B_other 11.798 r_long_range_B_refined 11.776 r_scangle_other 9.939 r_mcangle_it 7.266 r_mcangle_other 7.265 r_scbond_it 6.753 r_scbond_other 6.753 r_dihedral_angle_1_deg 5.908 r_mcbond_it 5.288 r_mcbond_other 5.287 r_angle_refined_deg 1.682 r_angle_other_deg 0.573 r_chiral_restr 0.08 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.006 r_bond_other_d r_dihedral_angle_4_deg 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 4354 Nucleic Acid Atoms Solvent Atoms 216 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling PHASER phasing