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Crystal structure of human Dbp5 in complex with AMPPNP and RNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J0S PDB ENTRY 2J0S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 100mM Tris pH 7.0, 20% PEG 2000 mono-methyl-ether, 3% PEG 3350, 30mM NaF, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.08 40.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.6 α = 90 b = 79.66 β = 90.02 c = 124.54 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 100 CCD MARRESEARCH 2007-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.00680 SLS X06SA
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 2.2 41.52 99.5 0.106 10.89 4.11 41194 41211 35.8
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) 1 2.2 2.3 99.3 0.273 4.54 4.11 5113
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 PDB ENTRY 2J0S 2.2 41.52 39149 2061 100 0.1713 0.16846 0.1715 0.22518 0.2191 RANDOM 21.053
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] 0.25 0.08 0.66 -0.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.661 r_dihedral_angle_4_deg 18.071 r_dihedral_angle_3_deg 15.626 r_dihedral_angle_1_deg 6.304 r_scangle_it 5.066 r_scbond_it 3.201 r_angle_refined_deg 1.855 r_mcangle_it 1.755 r_mcbond_it 0.934 r_chiral_restr 0.116
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.661 r_dihedral_angle_4_deg 18.071 r_dihedral_angle_3_deg 15.626 r_dihedral_angle_1_deg 6.304 r_scangle_it 5.066 r_scbond_it 3.201 r_angle_refined_deg 1.855 r_mcangle_it 1.755 r_mcbond_it 0.934 r_chiral_restr 0.116 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 6178 Nucleic Acid Atoms 237 Solvent Atoms 300 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing