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Crystal structure of Chitinase D from Serratia proteamaculans in complex with N-acetyl glucosamine at 1.93 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 43.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.211 α = 90 b = 74.918 β = 90 c = 87.049 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 RRCAT INDUS-2 BEAMLINE PX-BL21 0.97947 RRCAT INDUS-2 PX-BL21
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.93 59.22 100 0.134 0.125 8.6 29280 29280 18.8
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 1.93 2 95.7 0.301 2.6 29280
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 (All) 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 1.93 59.21 29280 28130 1504 99.4 0.16392 0.16392 0.16226 0.1746 0.19615 0.2037 RANDOM 16.393
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] 1.67 -0.86 -0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.707 r_dihedral_angle_4_deg 14.588 r_dihedral_angle_3_deg 14.057 r_dihedral_angle_1_deg 6.356 r_long_range_B_refined 6.139 r_long_range_B_other 6.138 r_scangle_other 3.479 r_scbond_it 2.225 r_scbond_other 2.225 r_mcangle_other 2.101
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.707 r_dihedral_angle_4_deg 14.588 r_dihedral_angle_3_deg 14.057 r_dihedral_angle_1_deg 6.356 r_long_range_B_refined 6.139 r_long_range_B_other 6.138 r_scangle_other 3.479 r_scbond_it 2.225 r_scbond_other 2.225 r_mcangle_other 2.101 r_mcangle_it 2.1 r_angle_refined_deg 1.909 r_mcbond_it 1.334 r_mcbond_other 1.329 r_angle_other_deg 0.903 r_chiral_restr 0.114 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3112 Nucleic Acid Atoms Solvent Atoms 442 Heterogen Atoms 31
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement AUTOMAR data reduction