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Crystal Structure of Family GH18 Chitinase from Cycas revoluta a Complex with Allosamidin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ALF PDB ENTRY 3ALF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 60% V/V TACSIMATE pH 7.0, 0.1M BIS-TRIS PROPANE pH 7.0, 0.06MM ALLOSAMIDIN, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.06 40.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.842 α = 90 b = 64.114 β = 90 c = 85.583 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 95 CCD ADSC QUANTUM 270 2014-02-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98 Photon Factory BL-17A
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 1.5 51.31 99.3 0.069 52.16 9.7 51423
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 1.5 1.53 98.2 0.418 8.6 9.1 22732
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 3ALF 1.5 50 48750 2610 99.17 0.182 0.18134 0.1826 0.19414 0.1958 RANDOM 11.749
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] 1.32 -0.55 -0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.923 r_dihedral_angle_4_deg 13.904 r_dihedral_angle_3_deg 11.568 r_dihedral_angle_1_deg 5.384 r_long_range_B_refined 2.807 r_long_range_B_other 2.628 r_angle_refined_deg 1.199 r_scangle_other 1.042 r_mcangle_it 0.9 r_mcangle_other 0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.923 r_dihedral_angle_4_deg 13.904 r_dihedral_angle_3_deg 11.568 r_dihedral_angle_1_deg 5.384 r_long_range_B_refined 2.807 r_long_range_B_other 2.628 r_angle_refined_deg 1.199 r_scangle_other 1.042 r_mcangle_it 0.9 r_mcangle_other 0.9 r_angle_other_deg 0.758 r_scbond_it 0.633 r_scbond_other 0.633 r_mcbond_it 0.504 r_mcbond_other 0.502 r_chiral_restr 0.067 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2679 Nucleic Acid Atoms Solvent Atoms 261 Heterogen Atoms 51
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling