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Human DEAD-box RNA helicase DDX20, Conserved domain I (DEAD) in complex with AMPPNP (Adenosine-(Beta,gamma)-imidotriphosphate)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OXC PDB entry 2OXC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 277 25% PEG 3350, 200mM Ammonium acetate, 100mM Bis-Tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.49 50.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.56 α = 90 b = 63.56 β = 90 c = 214.6 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 Mirrors 2007-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.00595 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.9 45 99.7 0.081 0.023 32.1 20.5 40642 40642
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 100 0.126 0.041 21.3 18.2 5705
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 2OXC 1.9 38.43 38606 38606 2032 100 0.17368 0.17368 0.17219 0.1766 0.20219 0.2067 RANDOM 14.938
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] -0.08 -0.04 -0.08 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.981 r_dihedral_angle_4_deg 18.811 r_dihedral_angle_3_deg 12.681 r_dihedral_angle_1_deg 5.321 r_scangle_it 3.273 r_scbond_it 2.405 r_angle_refined_deg 1.648 r_mcangle_it 1.273 r_mcbond_it 1.087 r_angle_other_deg 0.995
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.981 r_dihedral_angle_4_deg 18.811 r_dihedral_angle_3_deg 12.681 r_dihedral_angle_1_deg 5.321 r_scangle_it 3.273 r_scbond_it 2.405 r_angle_refined_deg 1.648 r_mcangle_it 1.273 r_mcbond_it 1.087 r_angle_other_deg 0.995 r_symmetry_hbond_refined 0.497 r_symmetry_vdw_other 0.352 r_mcbond_other 0.262 r_nbd_refined 0.212 r_nbd_other 0.193 r_nbtor_refined 0.17 r_xyhbond_nbd_refined 0.153 r_symmetry_vdw_refined 0.089 r_chiral_restr 0.084 r_nbtor_other 0.084 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3156 Nucleic Acid Atoms Solvent Atoms 315 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement MxCuBE data collection XDS data reduction XSCALE data scaling MOLREP phasing