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Crystal structure of bleomycin N-acetyltransferase from bleomycin-producing Streptomyces verticillus ATCC15003
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZW4 PDB ENTRY 2ZW4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 gel-tube counter diffusion 7.5 293 0.75% PEG 400, 1.0M ammonium sulfate, 0.1M Hepes
, pH 7.5, gel-tube counter diffusion, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.74 67.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.91 α = 90 b = 100.91 β = 90 c = 164.23 γ = 120
Symmetry Space Group P 31 2 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 2006-05-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0000 SPring-8 BL41XU
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 2.5 50 81.5 0.074 0.074 11.7 3.2 27705 27705 36
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) 2.5 2.59 57.2 0.271 0.271 2.3 1.6 1915
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) 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 PDB ENTRY 2ZW4 2.5 30 1 2 27662 27662 1353 81.1 0.211 0.211 0.2105 0.272 0.2722 RANDOM 44.3
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_dihedral_angle_d 27.7 x_scangle_it 10.6 x_scbond_it 7.73 x_mcangle_it 7.49 x_mcbond_it 5.01 x_angle_deg 1.3 x_improper_angle_d 0.61 x_bond_d 0.006 x_bond_d_na x_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 27.7 x_scangle_it 10.6 x_scbond_it 7.73 x_mcangle_it 7.49 x_mcbond_it 5.01 x_angle_deg 1.3 x_improper_angle_d 0.61 x_bond_d 0.006 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4461 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms 20
Software Software Software Name Purpose X-PLOR refinement BSS data collection HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing