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Crystal Structure of the PID-3 RRM domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7OCX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 0.03 M Sodium nitrate,
0.03 M Sodium phosphatedibasic
0.03 M Ammonium sulfate
0.1 M HEPES, 0.1 M MOPS pH 7.5
20% v/v PEG 500 MME;
10% w/v PEG 20000
Crystal Properties Matthews coefficient Solvent content 2.34 47.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.294 α = 90 b = 43.294 β = 90 c = 158.181 γ = 120
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 EIGER X 16M 2020-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.28 SLS X10SA
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 1.82 37.49 95.02 0.987 38.78 17.9 14314 24.56
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 1.82 1.885 0.436 0.56
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7OCX 1.82 36.48 1.39 14245 778 95.02 0.1838 0.1823 0.1814 0.2098 0.209 31.77
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 f_dihedral_angle_d 5.425 f_angle_d 0.8545 f_chiral_restr 0.0543 f_bond_d 0.005 f_plane_restr 0.0045
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1232 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 2
Software Software Software Name Purpose PHENIX refinement xia2 data reduction Aimless data scaling Coot model building PHASER phasing