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Crystal structure of the SPOC domain of human RBM15
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7Z1K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277.15 0.2M Sodium malonate dibasic monohydrate, 0.1M Bis-Tris propane 6.5, 20% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.16 42.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.031 α = 90 b = 65.98 β = 90 c = 116.808 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 EIGER X 16M 2019-05-05 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 1.45 57.45 100 0.112 0.116 0.999 12.9 3.5 62616 17.81
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 1.45 1.47 2.08 2.12 0.571
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 7Z1K 1.45 57.45 1.34 62507 3211 99.91 0.1983 0.1973 0.1969 0.2177 0.2177 26.06
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 5.5903 f_angle_d 0.8809 f_chiral_restr 0.0893 f_plane_restr 0.0083 f_bond_d 0.0058
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2535 Nucleic Acid Atoms Solvent Atoms 318 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement PHENIX refinement DIALS data reduction DIALS data scaling PHASER phasing