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Crystal structure of a class V chitinase from Arabidopsis thaliana
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ALF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 293 100mM trisodium citrate, 20% PEG10000, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.08 60.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.574 α = 73.63 b = 75.079 β = 73.34 c = 97.347 γ = 68.47
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 mirrors 2010-03-17 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 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 50 94.5 0.102 7.6 2.9 116512
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 2.03 88.7 0.336 1.9 2.3
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 MOLECULAR REPLACEMENT THROUGHOUT 3ALF 2.01 50 110709 5800 94.21 0.1978 0.19626 0.1965 0.22715 0.2263 RANDOM 12.842
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] 0.63 -0.28 0.66 -0.25 0.11 -0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.667 r_dihedral_angle_4_deg 17.117 r_dihedral_angle_3_deg 13.318 r_dihedral_angle_1_deg 5.635 r_scangle_it 2.329 r_scbond_it 1.425 r_angle_refined_deg 1.155 r_mcangle_it 1 r_mcbond_it 0.532 r_chiral_restr 0.077
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.667 r_dihedral_angle_4_deg 17.117 r_dihedral_angle_3_deg 13.318 r_dihedral_angle_1_deg 5.635 r_scangle_it 2.329 r_scbond_it 1.425 r_angle_refined_deg 1.155 r_mcangle_it 1 r_mcbond_it 0.532 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10564 Nucleic Acid Atoms Solvent Atoms 581 Heterogen Atoms 39
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling