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The crystal structure of a chitinase CrChi1 from the nematophagous fungus Clonostachys rosea
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W9P PDB ENTRY 1W9P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 291 0.2M ammonium dihydrogen phosphate, 15%(w/v) PEG 3350, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.12 41.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.088 α = 90 b = 71.715 β = 91.25 c = 59.075 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 IMAGE PLATE MAR scanner 345 mm plate osmic mirror 2008-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 1.8 50 95 0.081 34080 30889
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) 1.8 1.9 92.3 0.48
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 1W9P 1.8 45.59 30889 1651 95.22 0.21237 0.20997 0.2088 0.25739 0.2555 RANDOM 20.537
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] 0.6 -0.26 -0.41 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.902 r_dihedral_angle_4_deg 15.38 r_dihedral_angle_3_deg 14.974 r_dihedral_angle_1_deg 6.441 r_scangle_it 2.777 r_scbond_it 2.046 r_angle_refined_deg 1.556 r_mcangle_it 1.17 r_mcbond_it 0.793 r_symmetry_vdw_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.902 r_dihedral_angle_4_deg 15.38 r_dihedral_angle_3_deg 14.974 r_dihedral_angle_1_deg 6.441 r_scangle_it 2.777 r_scbond_it 2.046 r_angle_refined_deg 1.556 r_mcangle_it 1.17 r_mcbond_it 0.793 r_symmetry_vdw_refined 0.314 r_nbtor_refined 0.308 r_symmetry_hbond_refined 0.269 r_nbd_refined 0.22 r_xyhbond_nbd_refined 0.176 r_chiral_restr 0.099 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2964 Nucleic Acid Atoms Solvent Atoms 441 Heterogen Atoms
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling