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Sla1 SH3_3 domain (residues 355-414)
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 7.5 292 0.1M HEPES pH 7.5
20% PEG 10000
1mM peptide (PVSTPARTPARTPTP) dissolved in 0.03M HEPES pH 8, 0.15M NaCl, 0.5mM TCEP
Crystal Properties Matthews coefficient Solvent content 1.74 29.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.533 α = 90 b = 50.423 β = 90 c = 51.967 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-F 2024-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9762 PETRA III, EMBL c/o DESY P13 (MX1)
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 1.49 51.97 100 0.078 0.087 0.037 0.998 15.6 10 17131
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 1.49 1.52 99.9 0.422 0.473 0.211 0.943 4.8 9.3
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.491 36.214 17083 848 99.947 0.145 0.143 0.1421 0.1895 0.1888 RANDOM 18.897
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] -0.915 0.226 0.689
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.048 r_dihedral_angle_6_deg 16.885 r_dihedral_angle_3_deg 13.145 r_lrange_it 11.566 r_lrange_other 11.097 r_scangle_it 8.545 r_scangle_other 8.54 r_scbond_it 6.214 r_scbond_other 6.208 r_dihedral_angle_1_deg 6.153
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.048 r_dihedral_angle_6_deg 16.885 r_dihedral_angle_3_deg 13.145 r_lrange_it 11.566 r_lrange_other 11.097 r_scangle_it 8.545 r_scangle_other 8.54 r_scbond_it 6.214 r_scbond_other 6.208 r_dihedral_angle_1_deg 6.153 r_mcangle_other 5.995 r_mcangle_it 5.992 r_rigid_bond_restr 5.644 r_mcbond_it 4.4 r_mcbond_other 4.375 r_angle_refined_deg 1.965 r_angle_other_deg 0.664 r_nbd_refined 0.196 r_symmetry_nbd_other 0.194 r_symmetry_xyhbond_nbd_refined 0.19 r_nbtor_refined 0.18 r_symmetry_nbd_refined 0.157 r_xyhbond_nbd_refined 0.156 r_nbd_other 0.155 r_ncsr_local_group_1 0.147 r_chiral_restr 0.106 r_symmetry_nbtor_other 0.089 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 982 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling autoPROC data reduction PHENIX model building Coot model building MOLREP phasing