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Serratia marcescens Chitinase B complexed with macrolide inhibitor 29
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WD0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 0.1M Hepes-Na pH7.0, 0.8M ammonium sulfate, 5% (v/v) glycerol
Crystal Properties Matthews coefficient Solvent content 4.23 70.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.997 α = 90 b = 97.997 β = 90 c = 196.97 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2012-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.9800 Photon Factory BL-17A
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 2.35 40 100 0.149 16.1 8.9 40914 40914 -3 20
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 2.35 2.4 100 0.577 4.8 9.1
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 3WD0 2.35 39.3 38533 2033 99.39 0.16989 0.16839 0.1768 0.19797 0.2039 RANDOM 22.476
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] 0.3 0.3 -0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.648 r_dihedral_angle_4_deg 17.288 r_dihedral_angle_3_deg 12.762 r_dihedral_angle_1_deg 6.757 r_angle_refined_deg 1.409 r_angle_other_deg 0.698 r_chiral_restr 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.012 r_gen_planes_other 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.648 r_dihedral_angle_4_deg 17.288 r_dihedral_angle_3_deg 12.762 r_dihedral_angle_1_deg 6.757 r_angle_refined_deg 1.409 r_angle_other_deg 0.698 r_chiral_restr 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.012 r_gen_planes_other 0.003 r_bond_other_d 0.001 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3913 Nucleic Acid Atoms Solvent Atoms 257 Heterogen Atoms 85
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing Coot model building