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Crystal structure of glycopeptide hexose oxidase DBV29 complexed with teicoplanin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WDW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 17% PEG 3350, 0.2M diammonium hydrogen citrate, pH 5.0
Crystal Properties Matthews coefficient Solvent content 2.42 49.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.791 α = 90 b = 150.778 β = 98.4 c = 124.853 γ = 90
Symmetry Space Group P 1 21 1
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 315 2013-03-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1 NSRRC BL13B1
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 1.93 29.51 97.8 0.091 14.97 4.6 163843
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 1.93 1.96 97.1 0.573 2.87 4.6
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 2WDW 1.93 29.4 155630 8214 97.58 0.15842 0.15594 0.1685 0.20464 0.2132 RANDOM 32.621
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] -2.12 -1.06 -0.04 2.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.726 r_dihedral_angle_4_deg 17.994 r_dihedral_angle_3_deg 15.113 r_long_range_B_refined 9.135 r_long_range_B_other 9.135 r_dihedral_angle_1_deg 6.761 r_scangle_other 6.407 r_scbond_it 4.245 r_scbond_other 4.245 r_mcangle_it 3.956
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.726 r_dihedral_angle_4_deg 17.994 r_dihedral_angle_3_deg 15.113 r_long_range_B_refined 9.135 r_long_range_B_other 9.135 r_dihedral_angle_1_deg 6.761 r_scangle_other 6.407 r_scbond_it 4.245 r_scbond_other 4.245 r_mcangle_it 3.956 r_mcangle_other 3.956 r_mcbond_it 2.839 r_mcbond_other 2.822 r_angle_refined_deg 2.162 r_angle_other_deg 1.252 r_chiral_restr 0.134 r_bond_refined_d 0.022 r_gen_planes_refined 0.013 r_bond_other_d 0.004 r_gen_planes_other 0.003 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 16104 Nucleic Acid Atoms Solvent Atoms 1400 Heterogen Atoms 615
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing