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Crystal stricture of E145G/Y227F chitinase in complex with cyclo-(L-His-L-Pro) from Bacillus cereus NCTU2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3N12 PDB ENTRY 3N12
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 291 50mM potassium phosphate monobasic, 20%(w/v) PEG 8000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2 38.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.737 α = 90 b = 75.045 β = 90 c = 79.081 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 110 CCD ADSC QUANTUM 315 2009-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1.0000 NSRRC BL13B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 30 99.9 0.058 0.075 27.3 6.6 20188
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) 2 2.07 99.9 0.058 0.424 6.1 7 1969
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 3N12 2 29.73 19103 1031 99.52 0.20135 0.19934 0.1995 0.23751 0.2394 RANDOM 27.948
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] -1.43 0.85 0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.488 r_dihedral_angle_4_deg 12.8 r_dihedral_angle_3_deg 11.621 r_dihedral_angle_1_deg 4.287 r_scangle_it 0.926 r_angle_refined_deg 0.707 r_scbond_it 0.572 r_mcangle_it 0.482 r_mcbond_it 0.258 r_chiral_restr 0.049
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.488 r_dihedral_angle_4_deg 12.8 r_dihedral_angle_3_deg 11.621 r_dihedral_angle_1_deg 4.287 r_scangle_it 0.926 r_angle_refined_deg 0.707 r_scbond_it 0.572 r_mcangle_it 0.482 r_mcbond_it 0.258 r_chiral_restr 0.049 r_bond_refined_d 0.003 r_gen_planes_refined 0.002 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 2511 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 17
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling