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Crystal Structure of a chitinase from the Yersinia entomophaga toxin complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OA5 PDB entry 3OA5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 26% PEG 3350, 2% isopropanol,
0.1 M calcium chloride, 0.1 M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.43 49.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.505 α = 90 b = 210.556 β = 95.27 c = 92.584 γ = 90
Symmetry Space Group P 1 21 1
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 2009-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95369 Australian Synchrotron MX2
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 1.8 105.278 99.9 0.115 13.9 7.6 212127 212127
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) 1 1.8 1.9 100 0.582 0.582 1.2 7.2 30999
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 3OA5 1.8 105.278 212271 212074 10651 99.91 0.1617 0.1617 0.1598 0.1604 0.199 0.1997 RANDOM 14.8263
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] 0.95 0.06 -0.29 -0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.158 r_dihedral_angle_4_deg 19.161 r_dihedral_angle_3_deg 12.499 r_dihedral_angle_1_deg 6.428 r_scangle_it 5.039 r_scbond_it 3.324 r_mcangle_it 2.056 r_angle_refined_deg 2.004 r_mcbond_it 1.229 r_chiral_restr 0.161
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.158 r_dihedral_angle_4_deg 19.161 r_dihedral_angle_3_deg 12.499 r_dihedral_angle_1_deg 6.428 r_scangle_it 5.039 r_scbond_it 3.324 r_mcangle_it 2.056 r_angle_refined_deg 2.004 r_mcbond_it 1.229 r_chiral_restr 0.161 r_bond_refined_d 0.024 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16574 Nucleic Acid Atoms Solvent Atoms 1206 Heterogen Atoms 24
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection XDS data reduction