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X-ray structure of KH1-2 domain of IMP3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ANN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 292 0.08 M magnesium acetate, 0.05 M sodium cacodylate pH 6.5, 30% w/v Polyethylene glycol 4,000
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.2 α = 90 b = 58.09 β = 90 c = 60.87 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER X 16M 2018-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.000009 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.15 50 100 0.084 0.999 11.94 6.5 7366
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.21 99.9 0.8 0.767 1.63 6.9
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 2ann 2.15 42.02 6518 848 99.88 0.23976 0.23287 0.2578 0.29273 0.2903 RANDOM 39.272
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] -3.99 -2.14 6.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.448 r_dihedral_angle_3_deg 14.737 r_dihedral_angle_4_deg 14.547 r_dihedral_angle_1_deg 5.753 r_long_range_B_refined 4.617 r_long_range_B_other 4.615 r_mcangle_it 2.881 r_mcangle_other 2.88 r_scangle_other 2.735 r_mcbond_other 1.747
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.448 r_dihedral_angle_3_deg 14.737 r_dihedral_angle_4_deg 14.547 r_dihedral_angle_1_deg 5.753 r_long_range_B_refined 4.617 r_long_range_B_other 4.615 r_mcangle_it 2.881 r_mcangle_other 2.88 r_scangle_other 2.735 r_mcbond_other 1.747 r_mcbond_it 1.746 r_scbond_it 1.613 r_scbond_other 1.612 r_angle_refined_deg 1.251 r_angle_other_deg 0.899 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1272 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling Auto-Rickshaw phasing