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Serratia marcescens Chitinase B complexed with macrolide inhibitor 26
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 4.07 69.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.98 α = 90 b = 96.98 β = 90 c = 193.84 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 2012-01-30 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 2.6 40 99.6 0.101 16.2 11.8 29317 29200 -3 42.4
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 2.6 2.74 98.3 0.62 3.7 11.1
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 MAD THROUGHOUT 3WD0 2.6 40 27648 1479 99.48 0.23253 0.22934 0.2356 0.29371 0.29 RANDOM 49.539
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] 1.47 1.47 -2.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.189 r_dihedral_angle_4_deg 20.402 r_dihedral_angle_3_deg 15.357 r_long_range_B_refined 8.963 r_long_range_B_other 8.959 r_mcangle_other 6.655 r_mcangle_it 6.654 r_dihedral_angle_1_deg 6.41 r_scangle_other 6.333 r_mcbond_it 4.487
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.189 r_dihedral_angle_4_deg 20.402 r_dihedral_angle_3_deg 15.357 r_long_range_B_refined 8.963 r_long_range_B_other 8.959 r_mcangle_other 6.655 r_mcangle_it 6.654 r_dihedral_angle_1_deg 6.41 r_scangle_other 6.333 r_mcbond_it 4.487 r_mcbond_other 4.483 r_scbond_it 4.116 r_scbond_other 4.116 r_angle_refined_deg 1.59 r_angle_other_deg 0.84 r_chiral_restr 0.085 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_gen_planes_other 0.003 r_bond_other_d 0.002 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_scangle_it 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 87 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling MOLREP phasing Coot model building