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Crystal stricture of D143A chitinase in complex with NAG 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 2.03 39.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.717 α = 90 b = 76.752 β = 90 c = 78.502 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 1.00000 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 1.7 30 99.9 0.053 0.036 24.1 3.7 33132
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) 1.7 1.76 99.9 0.357 0.36 3.6 3.6 3253
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 1.7 24.77 31402 1671 99.92 0.18793 0.18677 0.1867 0.21022 0.2096 RANDOM 16.18
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] -0.78 -0.26 1.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.743 r_dihedral_angle_4_deg 12.764 r_dihedral_angle_3_deg 11.929 r_dihedral_angle_1_deg 5.239 r_scangle_it 1.942 r_scbond_it 1.22 r_angle_refined_deg 0.984 r_mcangle_it 0.718 r_mcbond_it 0.371 r_chiral_restr 0.067
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.743 r_dihedral_angle_4_deg 12.764 r_dihedral_angle_3_deg 11.929 r_dihedral_angle_1_deg 5.239 r_scangle_it 1.942 r_scbond_it 1.22 r_angle_refined_deg 0.984 r_mcangle_it 0.718 r_mcbond_it 0.371 r_chiral_restr 0.067 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 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 2506 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 29
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling