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Crystal structure of the Wss1 E203Q mutant from S. pombe
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JIG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 100 mM TRIS/HCl, 20% PEG 1000
Crystal Properties Matthews coefficient Solvent content 1.82 32.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.16 α = 90 b = 57.26 β = 113.01 c = 50.64 γ = 90
Symmetry Space Group P 1 21 1
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 PSI PILATUS 6M 2016-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.75 30 95.3 0.041 14.1 3.5 20977
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.85 94.6 0.431 2.7
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 (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 5JIG 1.75 15 19928 1049 95.52 0.17404 0.17256 0.1821 0.19541 0.2149 RANDOM 37.41
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] -2.09 -0.11 1.38 0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.428 r_sphericity_free 24.799 r_dihedral_angle_4_deg 14.076 r_dihedral_angle_3_deg 13.012 r_sphericity_bonded 6.911 r_dihedral_angle_1_deg 4.914 r_long_range_B_refined 3.597 r_long_range_B_other 3.286 r_mcangle_it 2.529 r_mcangle_other 2.528
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.428 r_sphericity_free 24.799 r_dihedral_angle_4_deg 14.076 r_dihedral_angle_3_deg 13.012 r_sphericity_bonded 6.911 r_dihedral_angle_1_deg 4.914 r_long_range_B_refined 3.597 r_long_range_B_other 3.286 r_mcangle_it 2.529 r_mcangle_other 2.528 r_scangle_other 2.46 r_scbond_it 2.396 r_scbond_other 2.383 r_mcbond_it 2.249 r_mcbond_other 2.239 r_rigid_bond_restr 1.242 r_angle_refined_deg 0.965 r_angle_other_deg 0.7 r_chiral_restr 0.057 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1893 Nucleic Acid Atoms Solvent Atoms 141 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing