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Room temperature crystal structure of a RNA binding motif protein 39 (Rbm39) from Mus musculus at 1.11 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3S6E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 277 20.00% polyethylene glycol 6000, 0.1M sodium citrate pH 5.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.01 38.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.617 α = 90 b = 52.829 β = 90 c = 85.652 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 296 PIXEL DECTRIS PILATUS 6M Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator 2012-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.11 28.551 94.2 0.055 18.4 9.7 75696 -3 10.629
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.11 1.14 57.9 1.016 2.2 5
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 3s6e 1.11 28.551 75639 3786 93.85 0.1134 0.1126 0.1264 0.1289 0.1403 RANDOM 17.5736
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] -0.04 0.21 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.094 r_dihedral_angle_3_deg 11.724 r_dihedral_angle_4_deg 10.869 r_sphericity_free 9.332 r_scangle_it 6.427 r_dihedral_angle_1_deg 5.249 r_sphericity_bonded 4.64 r_scbond_it 4.479 r_mcangle_it 3.868 r_mcbond_it 2.526
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.094 r_dihedral_angle_3_deg 11.724 r_dihedral_angle_4_deg 10.869 r_sphericity_free 9.332 r_scangle_it 6.427 r_dihedral_angle_1_deg 5.249 r_sphericity_bonded 4.64 r_scbond_it 4.479 r_mcangle_it 3.868 r_mcbond_it 2.526 r_rigid_bond_restr 1.553 r_angle_refined_deg 1.491 r_mcbond_other 1.483 r_angle_other_deg 1.118 r_chiral_restr 0.094 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1676 Nucleic Acid Atoms Solvent Atoms 184 Heterogen Atoms
Software Software Software Name Purpose MolProbity model building PDB_EXTRACT data extraction REFMAC refinement XSCALE data scaling XDS data reduction REFMAC phasing