☰ Navigation Tabs
Nontypeable Haemophillus influenzae SapA in open and closed conformations, in complex with double stranded RNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3M8U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 22% (w/v) PEG 3350, 0.25 M NaBr, 0.1 M Bis-Tris Propane pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.38 48.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.26 α = 90 b = 147.97 β = 90 c = 59.55 γ = 90
Symmetry Space Group P 21 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 PIXEL DECTRIS PILATUS 6M 2014-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.920 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 2.61 65.74 97.4 0.078 0.102 0.995 8.27 3.8 38239 52.506
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.61 2.68 96.3 0.588 0.764 0.563 1.5 2.068
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 3M8U 2.61 65.74 36274 1870 96.87 0.1991 0.1965 0.2053 0.2488 0.2576 RANDOM 57.766
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] -0.01 -0.61 0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.985 r_dihedral_angle_4_deg 18.862 r_dihedral_angle_3_deg 16.322 r_dihedral_angle_1_deg 6.76 r_angle_refined_deg 1.175 r_angle_other_deg 0.854 r_chiral_restr 0.062 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.985 r_dihedral_angle_4_deg 18.862 r_dihedral_angle_3_deg 16.322 r_dihedral_angle_1_deg 6.76 r_angle_refined_deg 1.175 r_angle_other_deg 0.854 r_chiral_restr 0.062 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8009 Nucleic Acid Atoms 728 Solvent Atoms 157 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction xia2 data scaling PHASER phasing PDB_EXTRACT data extraction Coot model building PHENIX model building XSCALE data scaling BALBES phasing