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Crystal structure of RBM38 in complex with single-stranded DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CQD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 289 0.1M Tris-HCl (pH8.0), 2M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 3.42 64.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.284 α = 90 b = 79.284 β = 90 c = 66.388 γ = 120
Symmetry Space Group P 31 2 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 DECTRIS EIGER X 16M 2018-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9792 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 50 98.8 0.056 0.06 0.02 16.8 9.4 16406 23.94
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 96.6 1.075 1.169 0.435 0.957 7.8
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 THROUGHOUT 2cqd 2.003 30.495 1.35 15952 802 96.22 0.1726 0.1708 0.1731 0.2057 0.2067 55.886
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 14.672 f_angle_d 0.821 f_chiral_restr 0.055 f_bond_d 0.008 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 663 Nucleic Acid Atoms 143 Solvent Atoms 127 Heterogen Atoms 10
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling PHENIX refinement PDB_EXTRACT data extraction PHASER phasing