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The structure of Sac-KARI protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XDZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 298 0.2 M Li2SO4 and 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.2 44.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.434 α = 90 b = 90.827 β = 90 c = 154.105 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 CCD RAYONIX MX300HE 2016-03-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1.0 NSRRC BL15A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.75 78.25 99.4 33.8 4.4 69217
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.81 98.7 2.7
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 4XDZ 1.75 41.062 65672 3479 99.21 0.17662 0.17456 0.1849 0.21585 0.2272 RANDOM 33.216
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] -0.23 -0.59 0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.641 r_dihedral_angle_4_deg 14.545 r_dihedral_angle_3_deg 14.521 r_long_range_B_refined 8.424 r_long_range_B_other 8.424 r_scangle_other 7.334 r_dihedral_angle_1_deg 5.776 r_scbond_it 5.04 r_scbond_other 5.039 r_mcangle_it 3.677
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.641 r_dihedral_angle_4_deg 14.545 r_dihedral_angle_3_deg 14.521 r_long_range_B_refined 8.424 r_long_range_B_other 8.424 r_scangle_other 7.334 r_dihedral_angle_1_deg 5.776 r_scbond_it 5.04 r_scbond_other 5.039 r_mcangle_it 3.677 r_mcangle_other 3.677 r_mcbond_it 2.889 r_mcbond_other 2.888 r_angle_refined_deg 2.05 r_angle_other_deg 1.104 r_chiral_restr 0.126 r_bond_refined_d 0.021 r_gen_planes_refined 0.01 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 5144 Nucleic Acid Atoms Solvent Atoms 468 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing