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Crystal structure of human acidic chitinase in complex with bisdionin C
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LG2 PDB ENTRY 1LG2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.4 75% SATURATED NACL, 0.1 M HEPES PH 7.4
Crystal Properties Matthews coefficient Solvent content 3.2 62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.207 α = 90 b = 149.066 β = 90 c = 152.082 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 CCD 2006-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.2 20 99.9 0.1 14.1 4.3 161985 33.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.25 99.9 0.7 2.7 4.2
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 PDB ENTRY 1LG2 2.22 20.07 160348 1631 99.15 0.18135 0.18089 0.1784 0.22761 0.2245 RANDOM 31.558
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] 0.66 -1.52 0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.611 r_dihedral_angle_4_deg 19.36 r_dihedral_angle_3_deg 16.739 r_dihedral_angle_1_deg 6.274 r_scangle_it 4.86 r_scbond_it 3.193 r_mcangle_it 1.993 r_angle_refined_deg 1.864 r_mcbond_it 1.081 r_chiral_restr 0.139
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.611 r_dihedral_angle_4_deg 19.36 r_dihedral_angle_3_deg 16.739 r_dihedral_angle_1_deg 6.274 r_scangle_it 4.86 r_scbond_it 3.193 r_mcangle_it 1.993 r_angle_refined_deg 1.864 r_mcbond_it 1.081 r_chiral_restr 0.139 r_bond_refined_d 0.022 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17898 Nucleic Acid Atoms Solvent Atoms 1057 Heterogen Atoms 384
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling