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Calpain small subunit 1, RNA-binding protein Hfq
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PHJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 293 Molecular Dimensions Pact premier screen condition D06: 0.1 M MMT, 25% PEG1500, pH 9.0
Crystal Properties Matthews coefficient Solvent content 2.48 50.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 147.607 α = 90 b = 147.607 β = 90 c = 147.607 γ = 90
Symmetry Space Group P 21 3
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 PILATUS3 6M 2017-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.32 66.02 100 0.114 0.116 0.999 19.2 22.1 46565 42.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.32 2.38 100 1.115 1.141 0.632 22.2
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 4PHJ 2.32 66.01 43741 2337 99.02 0.20328 0.20093 0.2046 0.2474 0.2486 RANDOM 51.223
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.188 r_dihedral_angle_4_deg 19.942 r_dihedral_angle_3_deg 19.456 r_dihedral_angle_1_deg 7.306 r_long_range_B_refined 5.849 r_long_range_B_other 5.841 r_scangle_other 3.768 r_mcangle_it 3.067 r_mcangle_other 3.067 r_scbond_it 2.404
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.188 r_dihedral_angle_4_deg 19.942 r_dihedral_angle_3_deg 19.456 r_dihedral_angle_1_deg 7.306 r_long_range_B_refined 5.849 r_long_range_B_other 5.841 r_scangle_other 3.768 r_mcangle_it 3.067 r_mcangle_other 3.067 r_scbond_it 2.404 r_scbond_other 2.4 r_mcbond_it 1.955 r_mcbond_other 1.952 r_angle_refined_deg 1.855 r_angle_other_deg 1.393 r_chiral_restr 0.099 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 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 7591 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing XDS data reduction