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Crystal structure of the SPRY domain of the human DEAD-box protein DDX1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TOJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 35 % (v/v) PEG 600, 0.1 M tri-Sodium-citrate pH 5.5 - crystals appeared after 3 days and grew as single crystals
Crystal Properties Matthews coefficient Solvent content 2.43 49.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.06 α = 90 b = 76.14 β = 90 c = 122.66 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 PSI PILATUS 6M 2012-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.06998 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 47.78 98.6 0.076 0.079 23.63 12.71 28891 -3 32.683
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.1 97.6 0.563 0.586 6.52 12.69
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 3toj 2 47.78 28891 1445 98.6 0.2015 0.1997 0.1998 0.2368 0.234 RANDOM 28.267
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] 1.25 0.25 -1.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.902 r_dihedral_angle_4_deg 23.326 r_dihedral_angle_3_deg 13.989 r_dihedral_angle_1_deg 5.913 r_scangle_it 2.457 r_scbond_it 1.639 r_angle_refined_deg 1.139 r_mcangle_it 1.065 r_mcbond_it 0.629 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.902 r_dihedral_angle_4_deg 23.326 r_dihedral_angle_3_deg 13.989 r_dihedral_angle_1_deg 5.913 r_scangle_it 2.457 r_scbond_it 1.639 r_angle_refined_deg 1.139 r_mcangle_it 1.065 r_mcbond_it 0.629 r_nbtor_refined 0.306 r_nbd_refined 0.185 r_symmetry_vdw_refined 0.173 r_symmetry_hbond_refined 0.144 r_xyhbond_nbd_refined 0.113 r_chiral_restr 0.085 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3002 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction PHASER phasing PDB_EXTRACT data extraction XSCALE data scaling Coot model building