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De novo designed S-locus Protein 11 (SP11)-like protein (P6522 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 4.4 293.15 0.16M ammonium sulfate, 0.08M Na-acetate (pH 4.4), 20% (v/v) glycerol
Crystal Properties Matthews coefficient Solvent content 2.27 45.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.3 α = 90 b = 64.3 β = 90 c = 126.221 γ = 120
Symmetry Space Group P 65 2 2
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 2M-F 2023-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.000 Photon Factory AR-NE3A
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 1.5 51 99.6 0.061 0.063 0.015 0.999 25.1 16.8 25451 16.12
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 1.5 1.53 0.965 1.05 0.399 0.609 1.6
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 1.5 51 24122 1263 99.6 0.18119 0.17951 0.184 0.21339 0.2174 RANDOM 24.563
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] -0.25 -0.12 -0.25 0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 12.618 r_dihedral_angle_3_deg 12.305 r_long_range_B_refined 7.565 r_long_range_B_other 7.512 r_scangle_other 6.393 r_dihedral_angle_1_deg 5.839 r_scbond_it 4.198 r_scbond_other 4.192 r_mcangle_it 2.606 r_mcangle_other 2.605
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 12.618 r_dihedral_angle_3_deg 12.305 r_long_range_B_refined 7.565 r_long_range_B_other 7.512 r_scangle_other 6.393 r_dihedral_angle_1_deg 5.839 r_scbond_it 4.198 r_scbond_other 4.192 r_mcangle_it 2.606 r_mcangle_other 2.605 r_angle_refined_deg 2.181 r_mcbond_it 1.994 r_mcbond_other 1.916 r_angle_other_deg 0.784 r_chiral_restr 0.092 r_bond_refined_d 0.013 r_gen_planes_other 0.011 r_gen_planes_refined 0.009 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 1101 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing