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Class IV chitinase structure from Picea abies at 2.25A
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 1.91 35.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.584 α = 90 b = 66.415 β = 90 c = 36.607 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 MARMOSAIC 225 mm CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8726 ESRF ID23-2
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 2.25 50 99.1 0.105 8202
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) 2.25 2.29 92.9 0.225
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) 2.25 36.61 7796 377 98.79 0.15713 0.15377 0.1529 0.22482 0.2209 RANDOM 14.472
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] 0.04 -0.08 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.08 r_dihedral_angle_3_deg 15.163 r_dihedral_angle_4_deg 6.604 r_dihedral_angle_1_deg 5.611 r_scangle_it 4.251 r_scbond_it 2.913 r_mcangle_it 1.721 r_angle_refined_deg 1.642 r_mcbond_it 0.974 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.08 r_dihedral_angle_3_deg 15.163 r_dihedral_angle_4_deg 6.604 r_dihedral_angle_1_deg 5.611 r_scangle_it 4.251 r_scbond_it 2.913 r_mcangle_it 1.721 r_angle_refined_deg 1.642 r_mcbond_it 0.974 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.247 r_nbd_refined 0.198 r_symmetry_hbond_refined 0.182 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.109 r_bond_refined_d 0.021 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1511 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms
Software Software Software Name Purpose MAR345dtb data collection REFMAC refinement DENZO data reduction SCALEPACK data scaling REFMAC phasing