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Crystal structure of the M295Y variant of Ssl1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4M3H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 50 mM HEPES pH 7.0, 1.4 M ammonium sulfate, 10 mM [Co(NH3)6]Cl3
Crystal Properties Matthews coefficient Solvent content 2.02 39.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.4 α = 90 b = 104.24 β = 90 c = 162.06 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 2019-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.0 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.68 49.043 99.3 0.997 8.87 1.9 98807
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.684 1.692 0.572
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 NONE 4M3H 1.684 49.043 98712 4943 99.271 0.193 0.1906 0.1932 0.232 0.2349 25.32
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] -1.875 0.048 1.826
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_3_deg 35.009 r_dihedral_angle_2_deg 28.806 r_dihedral_angle_4_deg 16.178 r_dihedral_angle_3_deg 13.393 r_dihedral_angle_1_deg 7.561 r_lrange_it 6.15 r_lrange_other 6.149 r_scangle_it 4.097 r_scangle_other 4.064 r_mcangle_it 3.383
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_3_deg 35.009 r_dihedral_angle_2_deg 28.806 r_dihedral_angle_4_deg 16.178 r_dihedral_angle_3_deg 13.393 r_dihedral_angle_1_deg 7.561 r_lrange_it 6.15 r_lrange_other 6.149 r_scangle_it 4.097 r_scangle_other 4.064 r_mcangle_it 3.383 r_mcangle_other 3.383 r_scbond_it 2.952 r_scbond_other 2.902 r_mcbond_it 2.272 r_mcbond_other 2.272 r_angle_refined_deg 1.628 r_angle_other_deg 1.402 r_metal_ion_refined 0.226 r_nbd_refined 0.195 r_symmetry_nbd_other 0.191 r_nbd_other 0.186 r_symmetry_nbd_refined 0.18 r_nbtor_refined 0.167 r_symmetry_xyhbond_nbd_refined 0.144 r_xyhbond_nbd_refined 0.142 r_symmetry_xyhbond_nbd_other 0.134 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.078 r_symmetry_metal_ion_refined 0.027 r_bond_refined_d 0.012 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 6250 Nucleic Acid Atoms Solvent Atoms 632 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing