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Class IV chitinase structure from Picea abies at 1.55A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HBD Structure of Picea abies chitinase (PDB entry 3HBD)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 296 20% w/v polyethylene glycol 3000, 0.1M citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 1.87 34.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.194 α = 90 b = 65.792 β = 90 c = 36.496 γ = 90
Symmetry Space Group P 21 21 2
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 QUANTUM 315r 2006-03-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.9395 ESRF ID14-4
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 1.55 50 97.4 0.088 16.7 23744
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) 1.55 1.63 92.6 0.219 6.3
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 REFMAC 5.2.0019 rigidbody refinement THROUGHOUT Structure of Picea abies chitinase (PDB entry 3HBD) 1.55 50 22318 1202 97.05 0.16419 0.16261 0.1612 0.19382 0.1901 RANDOM 14.49
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] 0.53 -0.32 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.844 r_dihedral_angle_3_deg 11.903 r_dihedral_angle_1_deg 4.298 r_dihedral_angle_4_deg 3.297 r_scangle_it 2.94 r_scbond_it 1.909 r_mcangle_it 1.144 r_angle_refined_deg 1.045 r_mcbond_it 0.717 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.844 r_dihedral_angle_3_deg 11.903 r_dihedral_angle_1_deg 4.298 r_dihedral_angle_4_deg 3.297 r_scangle_it 2.94 r_scbond_it 1.909 r_mcangle_it 1.144 r_angle_refined_deg 1.045 r_mcbond_it 0.717 r_nbtor_refined 0.306 r_nbd_refined 0.204 r_symmetry_vdw_refined 0.172 r_symmetry_hbond_refined 0.146 r_xyhbond_nbd_refined 0.114 r_chiral_restr 0.069 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1567 Nucleic Acid Atoms Solvent Atoms 226 Heterogen Atoms 11
Software Software Software Name Purpose ADSC data collection REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing