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Crystal Structure of human splicing factor dim2/TXNL4B
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XBS PDB ENTRY 1XBS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 18% PEG8000, 0.2 M magnesium acetate tetrahydate, 0.1 M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.89 34.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.325 α = 90 b = 63.64 β = 92.29 c = 51.148 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD MARMOSAIC 300 mm CCD 2005-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.327 30.567 97 58146 56401 2 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRY 1XBS 1.327 30.567 56401 54157 2164 92.96 0.1303 0.1279 0.1378 0.1849 0.189 RANDOM 23.1496
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] -1.2 0.24 1.32 -0.14
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 59.449 r_dihedral_angle_2_deg 36.005 r_dihedral_angle_4_deg 30.328 r_sphericity_bonded 18.237 r_dihedral_angle_3_deg 14.179 r_dihedral_angle_1_deg 5.979 r_rigid_bond_restr 5.896 r_mcangle_it 3.396 r_mcbond_it 3.004 r_mcbond_other 2.979
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 59.449 r_dihedral_angle_2_deg 36.005 r_dihedral_angle_4_deg 30.328 r_sphericity_bonded 18.237 r_dihedral_angle_3_deg 14.179 r_dihedral_angle_1_deg 5.979 r_rigid_bond_restr 5.896 r_mcangle_it 3.396 r_mcbond_it 3.004 r_mcbond_other 2.979 r_angle_refined_deg 2.189 r_angle_other_deg 1.079 r_chiral_restr 0.141 r_bond_refined_d 0.022 r_gen_planes_refined 0.012 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2239 Nucleic Acid Atoms Solvent Atoms 382 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection DENZO data reduction SCALEPACK data scaling HKL-2000 data scaling PHASER phasing