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Crystal structure of the Helicase domain of human DDX25 RNA helicase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FUK PDB entry 1FUK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.1 M Bis-Tris propane, 2.5 M Ammonium sulfate pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.87 57.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.31 α = 90 b = 70.31 β = 90 c = 187.12 γ = 90
Symmetry Space Group P 43 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 IMAGE PLATE MACSCIENCE mirrors 2006-01-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.95373 BESSY 14.2
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 2.8 20 0.107 15.65 8.8 12185 12185 64.1
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) 2.8 2.9 100 0.82 2.59 9.1 1184
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 (All) 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 1FUK 2.8 19.44 11208 11208 974 100 0.23607 0.23607 0.23338 0.2772 0.26655 0.29 RANDOM 82.026
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] -0.22 -0.22 0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.818 r_dihedral_angle_4_deg 22.595 r_dihedral_angle_3_deg 18.195 r_dihedral_angle_1_deg 6.446 r_scangle_it 1.573 r_angle_refined_deg 1.244 r_scbond_it 0.926 r_mcangle_it 0.721 r_mcbond_it 0.389 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.818 r_dihedral_angle_4_deg 22.595 r_dihedral_angle_3_deg 18.195 r_dihedral_angle_1_deg 6.446 r_scangle_it 1.573 r_angle_refined_deg 1.244 r_scbond_it 0.926 r_mcangle_it 0.721 r_mcbond_it 0.389 r_nbtor_refined 0.311 r_symmetry_vdw_refined 0.275 r_nbd_refined 0.225 r_symmetry_hbond_refined 0.186 r_xyhbond_nbd_refined 0.137 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2623 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing