☰ Navigation Tabs
Crystal structure of Vibrio harveyi chitinase A complexed with hexasaccharide
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 2.22 44.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.704 α = 90 b = 83.323 β = 90 c = 106.565 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++ 2006-01-23 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 1.8 30 99.7 0.07 0.074 26.3 8.5 53131 53131 26.3 15.9
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 1.847 99 0.312 0.332 6.1 8.4 7564
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 1.8 30 53131 50392 2678 99.65 0.18223 0.18223 0.18076 0.1798 0.21013 0.21 RANDOM 15.433
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] 0.15 0.07 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.225 r_dihedral_angle_3_deg 11.961 r_dihedral_angle_4_deg 9.499 r_dihedral_angle_1_deg 5.103 r_scangle_it 1.267 r_angle_refined_deg 0.99 r_scbond_it 0.844 r_mcangle_it 0.637 r_mcbond_it 0.375 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.225 r_dihedral_angle_3_deg 11.961 r_dihedral_angle_4_deg 9.499 r_dihedral_angle_1_deg 5.103 r_scangle_it 1.267 r_angle_refined_deg 0.99 r_scbond_it 0.844 r_mcangle_it 0.637 r_mcbond_it 0.375 r_nbtor_refined 0.304 r_nbd_refined 0.177 r_symmetry_vdw_refined 0.144 r_xyhbond_nbd_refined 0.099 r_chiral_restr 0.069 r_symmetry_hbond_refined 0.066 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 690 Heterogen Atoms 85
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection MOSFLM data reduction SCALA data scaling AMoRE phasing