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Crystal Structure of Chitinase D from Serratia proteamaculans in complex with N-acetyl glucosamine, a hydrolyzed product of hexasaccharide at 1.7 Angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LGX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 298 2M SODIUM FORMATE, 0.1M SODIUM ACETATE, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.19 43.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.418 α = 90 b = 74.064 β = 90 c = 88.745 γ = 90
Symmetry Space Group P 2 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 77 CCD MARMOSAIC 225 mm CCD Mirrors 2013-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97 ESRF BM14
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 1.7 59.42 100 0.034 5.5 43061 43061
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 1.7 1.76 99.2 0.89 2.1
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 4LGX 1.7 59.42 43061 41221 2174 99.04 0.16841 0.16713 0.1792 0.1927 0.207 RANDOM 18.977
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] 0.49 -0.64 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.491 r_dihedral_angle_4_deg 15.249 r_dihedral_angle_3_deg 14.156 r_dihedral_angle_1_deg 6.173 r_long_range_B_refined 6.164 r_long_range_B_other 6.164 r_scangle_other 4.509 r_scbond_other 2.926 r_scbond_it 2.915 r_mcangle_it 2.672
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.491 r_dihedral_angle_4_deg 15.249 r_dihedral_angle_3_deg 14.156 r_dihedral_angle_1_deg 6.173 r_long_range_B_refined 6.164 r_long_range_B_other 6.164 r_scangle_other 4.509 r_scbond_other 2.926 r_scbond_it 2.915 r_mcangle_it 2.672 r_mcangle_other 2.571 r_angle_refined_deg 1.928 r_mcbond_it 1.769 r_mcbond_other 1.753 r_angle_other_deg 0.954 r_chiral_restr 0.117 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_bond_other_d 0.006 r_gen_planes_other 0.001 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 3112 Nucleic Acid Atoms Solvent Atoms 336 Heterogen Atoms 31
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling