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Complex of vancomycin with DI-acetyl-LYS-D-ALA-D-ALA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AA5 PDB ENTRY 1AA5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 CRYSTALS WERE PREPARED AT 293K FROM A SOLUTION CONTAINING 6.6 MM VANCOMYCIN, 6.6 MM DI- ACETYL-LYS -D-ALA-D-ALA, 3.3 % (V/V) ETHANOL, AND 0.66 M TRIS BUFFER PH 8.5, BY EQUILIBRATING THE SOLUTION AGAINST A RESERVOIR SOLUTION CONTAINING 10 % (V/V) ETHANOL AND 0.2 M TRIS BUFFER PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293.0K
Crystal Properties Matthews coefficient Solvent content 1.95 37.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.637 α = 90 b = 36.425 β = 90 c = 65.728 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 120 CCD ADSC QUAMTUM 4R MIRRORS 2000-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A Photon Factory BL-6A
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 25.5 100 0.046 0.043 11.7 6.8 8400 6.8
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 1.9 99.9 0.072 0.066 8.5 6.3
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 1AA5 1.8 5 4 7864 99 0.144 0.144 8.5
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]
RMS Deviations Key Refinement Restraint Deviation x_scangle_it 1.97 x_scbond_it 1.35 x_improper_angle_d 1.34 x_angle_deg 1.05 x_dihedral_angle_d 0.76 x_bond_d 0.009 x_bond_d_na x_bond_d_prot x_angle_d x_angle_d_na
RMS Deviations Key Refinement Restraint Deviation x_scangle_it 1.97 x_scbond_it 1.35 x_improper_angle_d 1.34 x_angle_deg 1.05 x_dihedral_angle_d 0.76 x_bond_d 0.009 x_bond_d_na x_bond_d_prot x_angle_d x_angle_d_na x_angle_d_prot x_angle_deg_na x_angle_deg_prot x_dihedral_angle_d_na x_dihedral_angle_d_prot x_improper_angle_d_na x_improper_angle_d_prot x_mcbond_it x_mcangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 636 Nucleic Acid Atoms Solvent Atoms 112 Heterogen Atoms 126
Software Software Software Name Purpose AMoRE phasing X-PLOR refinement MOSFLM data reduction CCP4 data scaling