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Complex with chitin oligomer of C-type lysozyme from the upper gastrointestinal tract of Opisthocomus hoatzin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6T5S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 3.5 293 0.1 M Citric acid pH 3.5, 3.0 M Sodium chloride, Hampton research INDEX screen no 7.
Crystal Properties Matthews coefficient Solvent content 2.31 46.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.051 α = 90 b = 55.008 β = 90 c = 65.829 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 ADSC QUANTUM 315 2012-09-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 1.25 42.247 99.9 0.105 0.998 13.4 8 38043
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 1.25 1.27 0.882 0.535
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE 6T5S 1.25 42.247 37953 1886 99.905 0.109 0.1078 0.1078 0.1343 0.1344 12.994
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] 0.21 -0.235 0.025
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.84 r_rigid_bond_restr 14.052 r_dihedral_angle_3_deg 12.246 r_dihedral_angle_4_deg 11.047 r_dihedral_angle_1_deg 6.406 r_lrange_it 4.274 r_scangle_it 3.951 r_scangle_other 3.949 r_lrange_other 3.869 r_scbond_it 3.464
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.84 r_rigid_bond_restr 14.052 r_dihedral_angle_3_deg 12.246 r_dihedral_angle_4_deg 11.047 r_dihedral_angle_1_deg 6.406 r_lrange_it 4.274 r_scangle_it 3.951 r_scangle_other 3.949 r_lrange_other 3.869 r_scbond_it 3.464 r_scbond_other 3.464 r_angle_other_deg 3.282 r_angle_refined_deg 2.191 r_mcangle_other 1.744 r_mcangle_it 1.69 r_mcbond_it 1.288 r_mcbond_other 1.251 r_symmetry_xyhbond_nbd_refined 0.274 r_xyhbond_nbd_refined 0.268 r_symmetry_nbd_refined 0.263 r_nbd_refined 0.252 r_symmetry_nbd_other 0.234 r_nbtor_refined 0.179 r_nbd_other 0.178 r_chiral_restr 0.164 r_symmetry_nbtor_other 0.12 r_symmetry_xyhbond_nbd_other 0.069 r_bond_other_d 0.036 r_bond_refined_d 0.018 r_gen_planes_other 0.018 r_gen_planes_refined 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1016 Nucleic Acid Atoms Solvent Atoms 205 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling Coot model building