☰ Navigation Tabs
Crystal structure of Vibrio harveyi chitinase A complexed with pentasaccharide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3B9E PDB ENTRY 3B9E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 288 16% (w/v) PEG 4000, 0.1M magnesium chloride, 0.1M HEPES pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 2.18 43.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.508 α = 90 b = 83.076 β = 90 c = 105.586 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 100 IMAGE PLATE RIGAKU RAXIS IV++ 2006-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
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 1.72 24.54 99.2 0.071 0.077 26.3 6.8 59561 59561 17.2
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 1.72 1.81 95.6 0.123 0.136 9.9 5.6 8247
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 3B9E 1.72 24.54 59561 56474 3024 99.16 0.18841 0.18841 0.18703 0.1853 0.2145 0.2116 RANDOM 15.683
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] -0.2 -0.19 0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.291 r_dihedral_angle_3_deg 12.033 r_dihedral_angle_4_deg 9.327 r_dihedral_angle_1_deg 5.146 r_scangle_it 1.337 r_angle_refined_deg 0.962 r_scbond_it 0.923 r_mcangle_it 0.648 r_mcbond_it 0.491 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.291 r_dihedral_angle_3_deg 12.033 r_dihedral_angle_4_deg 9.327 r_dihedral_angle_1_deg 5.146 r_scangle_it 1.337 r_angle_refined_deg 0.962 r_scbond_it 0.923 r_mcangle_it 0.648 r_mcbond_it 0.491 r_nbtor_refined 0.302 r_nbd_refined 0.17 r_symmetry_vdw_refined 0.167 r_symmetry_hbond_refined 0.129 r_xyhbond_nbd_refined 0.087 r_chiral_restr 0.07 r_bond_refined_d 0.006 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4353 Nucleic Acid Atoms Solvent Atoms 664 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection MOSFLM data reduction SCALA data scaling AMoRE phasing