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Crystal structure of wild-type chitinase A from Vibrio harveyi
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3B9E PDB ENTRY 3B9E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 288 1.20M Ammonium Sulfate, 0.1M Tris-HCl pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 2.3 46.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.267 α = 91.74 b = 64.283 β = 91.18 c = 83.522 γ = 112.91
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ 2006-01-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
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 2 24.62 94.6 0.066 0.076 19.5 4 73693 73693 19.5 17.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.11 91.9 0.228 0.263 5.5 4 10404
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 PDB ENTRY 3B9E 2 24.62 73693 69969 3724 94.61 0.17022 0.17022 0.16836 0.1695 0.2051 0.2075 RANDOM 16.188
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] 0.37 -0.71 0.3 -0.97 -0.21 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.885 r_dihedral_angle_3_deg 12.437 r_dihedral_angle_4_deg 10.338 r_dihedral_angle_1_deg 5.165 r_scangle_it 1.421 r_angle_refined_deg 0.968 r_scbond_it 0.946 r_mcangle_it 0.597 r_mcbond_it 0.453 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.885 r_dihedral_angle_3_deg 12.437 r_dihedral_angle_4_deg 10.338 r_dihedral_angle_1_deg 5.165 r_scangle_it 1.421 r_angle_refined_deg 0.968 r_scbond_it 0.946 r_mcangle_it 0.597 r_mcbond_it 0.453 r_nbtor_refined 0.301 r_nbd_refined 0.175 r_symmetry_hbond_refined 0.153 r_symmetry_vdw_refined 0.149 r_xyhbond_nbd_refined 0.112 r_chiral_restr 0.067 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8708 Nucleic Acid Atoms Solvent Atoms 1091 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection MOSFLM data reduction SCALA data scaling AMoRE phasing