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Crystal Structure of Sam0.7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 20% w/v PEG3350, 200 mM KSCN
Crystal Properties Matthews coefficient Solvent content 1.8 31.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.554 α = 90 b = 40.554 β = 90 c = 253.117 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 EIGER2 X 16M 2021-09-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.000 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.8 35.12 100 0.103 0.999 19 32.77 12505
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.91 99.9 1.623 0.965 1.65 34.94
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE computational model 1.8 35.12 12505 626 99.984 0.259 0.2571 0.2605 0.2961 0.3055 49.962
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] 1.573 0.787 1.573 -5.103
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.92 r_dihedral_angle_4_deg 19.291 r_dihedral_angle_3_deg 17.273 r_dihedral_angle_1_deg 6.615 r_lrange_it 5.337 r_lrange_other 5.335 r_scangle_it 3.873 r_scangle_other 3.87 r_scbond_it 2.596 r_scbond_other 2.593
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.92 r_dihedral_angle_4_deg 19.291 r_dihedral_angle_3_deg 17.273 r_dihedral_angle_1_deg 6.615 r_lrange_it 5.337 r_lrange_other 5.335 r_scangle_it 3.873 r_scangle_other 3.87 r_scbond_it 2.596 r_scbond_other 2.593 r_mcangle_it 2.561 r_mcangle_other 2.559 r_angle_refined_deg 1.959 r_mcbond_other 1.857 r_mcbond_it 1.855 r_angle_other_deg 1.332 r_nbd_refined 0.205 r_xyhbond_nbd_refined 0.205 r_symmetry_nbd_other 0.196 r_nbtor_refined 0.177 r_symmetry_nbd_refined 0.136 r_nbd_other 0.131 r_symmetry_xyhbond_nbd_refined 0.093 r_chiral_restr 0.092 r_symmetry_nbtor_other 0.083 r_symmetry_xyhbond_nbd_other 0.08 r_bond_refined_d 0.023 r_gen_planes_refined 0.015 r_bond_other_d 0.006 r_gen_planes_other 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 921 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing