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YZwIdeal x16 a scaffold for cryo-EM of small proteins of interest crystallizing in space group 19 (P 21 21 21)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8CPL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 50% w/v PEG200, 0.2M MgCl2 and 0.1M Sodium Cacodylate buffer pH 6.5
Crystal Properties Matthews coefficient Solvent content 3.29 62.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.26 α = 90 b = 196.76 β = 90 c = 208.053 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 EIGER X 16M 2022-09-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.976246 MAX IV BioMAX
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 2.217 48.91 41.1 0.167 0.182 0.07 0.997 8.1 6.6 61481
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 2.217 2.425 8.8 1.041 1.156 0.49 0.665 1.68 5.12
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 2.22 48.91 58551 2928 41.07 0.18846 0.18628 0.1949 0.23039 0.2327 RANDOM 32.657
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] -0.19 0.84 -0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.532 r_dihedral_angle_4_deg 19.156 r_dihedral_angle_3_deg 16.749 r_long_range_B_refined 9.636 r_long_range_B_other 9.388 r_dihedral_angle_1_deg 6.251 r_scangle_other 5.235 r_mcangle_it 4.266 r_mcangle_other 4.266 r_scbond_it 3.184
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.532 r_dihedral_angle_4_deg 19.156 r_dihedral_angle_3_deg 16.749 r_long_range_B_refined 9.636 r_long_range_B_other 9.388 r_dihedral_angle_1_deg 6.251 r_scangle_other 5.235 r_mcangle_it 4.266 r_mcangle_other 4.266 r_scbond_it 3.184 r_scbond_other 3.184 r_mcbond_it 2.699 r_mcbond_other 2.695 r_angle_refined_deg 1.464 r_angle_other_deg 1.243 r_chiral_restr 0.06 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 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 14315 Nucleic Acid Atoms Solvent Atoms 1507 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement STARANISO data scaling XDS data reduction PHASER phasing