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Crystal structure of a RNA binding motif protein 39 (RBM39) from Homo sapiens at 1.28 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CQ4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 20% polyethylene glycol 3350, 0.20M sodium fluoride, 1mM RNA-6b UAAUAA
Crystal Properties Matthews coefficient Solvent content 1.96 37.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.574 α = 90 b = 26.711 β = 90 c = 35.015 γ = 90
Symmetry Space Group P 21 21 2
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 PILATUS 6M Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing) 2013-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 1.0 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.28 32.461 92.2 0.023 0.027 0.013 27.7 3.9 20012 20012
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.28 1.35 63 0.285 0.285 0.355 0.205 2.7 2.3 1948
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 2CQ4 1.28 32.461 19974 1038 92.11 0.1487 0.1463 0.1489 0.1942 0.1927 RANDOM 21.6503
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] -0.54 -0.89 1.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.951 r_dihedral_angle_4_deg 16.028 r_dihedral_angle_3_deg 10.413 r_sphericity_free 8.26 r_scangle_it 6.737 r_scbond_it 4.776 r_dihedral_angle_1_deg 4.455 r_mcangle_it 4.45 r_sphericity_bonded 4.145 r_mcbond_it 2.968
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.951 r_dihedral_angle_4_deg 16.028 r_dihedral_angle_3_deg 10.413 r_sphericity_free 8.26 r_scangle_it 6.737 r_scbond_it 4.776 r_dihedral_angle_1_deg 4.455 r_mcangle_it 4.45 r_sphericity_bonded 4.145 r_mcbond_it 2.968 r_rigid_bond_restr 2.005 r_angle_refined_deg 1.698 r_mcbond_other 1.595 r_angle_other_deg 0.887 r_chiral_restr 0.096 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 666 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms
Software Software Software Name Purpose PDB_EXTRACT data extraction PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling SCALA data scaling