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Crystal structure of the human HSP40 DNAJB1-CTDs in complex with a peptide of NudC
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AGY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 298 0.1 M of sodium acetate trihydrate and 15% (v/v) of polyethylene glycol 400
Crystal Properties Matthews coefficient Solvent content 3.5 64.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.3 α = 90 b = 128.264 β = 90 c = 135.213 γ = 90
Symmetry Space Group I 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 193 PIXEL DECTRIS PILATUS 2M-F 2020-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0 SLS X06DA
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 2.54 46.53 99.9 0.14 0.99 16.5 13 12295
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 2.54 2.65 0.66
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 3AGY 2.541 46.53 12295 607 99.911 0.235 0.2328 0.2344 0.2681 0.2686 69.028
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] -3.914 2.607 1.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.139 r_dihedral_angle_4_deg 21.374 r_dihedral_angle_3_deg 18.674 r_dihedral_angle_1_deg 8.467 r_lrange_it 5.915 r_lrange_other 5.914 r_scangle_it 3.895 r_scangle_other 3.895 r_mcangle_it 3.57 r_mcangle_other 3.568
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.139 r_dihedral_angle_4_deg 21.374 r_dihedral_angle_3_deg 18.674 r_dihedral_angle_1_deg 8.467 r_lrange_it 5.915 r_lrange_other 5.914 r_scangle_it 3.895 r_scangle_other 3.895 r_mcangle_it 3.57 r_mcangle_other 3.568 r_scbond_it 2.4 r_scbond_other 2.399 r_mcbond_it 2.247 r_mcbond_other 2.243 r_angle_refined_deg 1.799 r_angle_other_deg 1.154 r_nbd_refined 0.206 r_nbd_other 0.201 r_symmetry_nbd_other 0.187 r_symmetry_nbd_refined 0.173 r_nbtor_refined 0.158 r_xyhbond_nbd_refined 0.137 r_symmetry_xyhbond_nbd_refined 0.129 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.065 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1430 Nucleic Acid Atoms Solvent Atoms 22 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing