☰ Navigation Tabs
Crystal structure of the nucleoporin Nup214 in complex with the DEAD-box helicase Ddx19
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FMO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9.5 298 PEG 3000, CHES buffer, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.38 48.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.369 α = 90 b = 112.915 β = 89.86 c = 142.573 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 ADSC QUANTUM 315 2008-05-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 0.9795 ALS 8.2.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.2 50 91.3 0.113 14.3 6.8 32548 29717 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.31 70.9 0.395 3.6 5.9 3249
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 3FMO 3.19 50 30998 28125 1504 90.73 0.25114 0.24938 0.2497 0.28317 0.276 RANDOM 72.611
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] 16.88 0.93 -3.14 -13.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.135 r_dihedral_angle_3_deg 18.342 r_dihedral_angle_4_deg 16.856 r_dihedral_angle_1_deg 7.528 r_angle_refined_deg 1.471 r_scangle_it 1.047 r_angle_other_deg 0.899 r_scbond_it 0.688 r_mcangle_it 0.411 r_mcbond_it 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.135 r_dihedral_angle_3_deg 18.342 r_dihedral_angle_4_deg 16.856 r_dihedral_angle_1_deg 7.528 r_angle_refined_deg 1.471 r_scangle_it 1.047 r_angle_other_deg 0.899 r_scbond_it 0.688 r_mcangle_it 0.411 r_mcbond_it 0.308 r_symmetry_vdw_other 0.269 r_nbd_refined 0.229 r_nbd_other 0.201 r_symmetry_vdw_refined 0.197 r_nbtor_refined 0.19 r_xyhbond_nbd_refined 0.167 r_symmetry_hbond_refined 0.151 r_nbtor_other 0.091 r_chiral_restr 0.08 r_mcbond_other 0.069 r_xyhbond_nbd_other 0.026 r_bond_refined_d 0.013 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10162 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 54
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling