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Crystal structure of Chitinase D from Serratia proteamaculans at 1.45 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 2.2 44.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.334 α = 90 b = 75.276 β = 90 c = 86.713 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 MARRESEARCH Mirror 2013-06-21 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 1.45 59.4 100 0.099 9.8 69368 69368
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 1.45 1.5 99.9 0.316 2
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 4LGX 1.45 59.4 65876 3503 99.83 0.20006 0.19935 0.2071 0.21299 0.2194 RANDOM 12.495
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] 0.81 -0.14 -0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.479 r_dihedral_angle_4_deg 13.764 r_dihedral_angle_3_deg 11.501 r_dihedral_angle_1_deg 6.079 r_long_range_B_refined 5.483 r_long_range_B_other 5.482 r_scangle_other 1.721 r_angle_refined_deg 1.457 r_mcangle_other 1.326 r_mcangle_it 1.325
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.479 r_dihedral_angle_4_deg 13.764 r_dihedral_angle_3_deg 11.501 r_dihedral_angle_1_deg 6.079 r_long_range_B_refined 5.483 r_long_range_B_other 5.482 r_scangle_other 1.721 r_angle_refined_deg 1.457 r_mcangle_other 1.326 r_mcangle_it 1.325 r_scbond_it 1.069 r_scbond_other 1.068 r_mcbond_it 0.776 r_angle_other_deg 0.772 r_mcbond_other 0.771 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001 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 587 Heterogen Atoms 22
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling