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Crystal structure of Aclacinomycin-10-hydroxylase (RdmB) in complex with Sinefungin (SFG)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QZZ RdmB+SAM complex
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 294 ammonium acetate, PEG 4000, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.17 43.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.758 α = 90 b = 86.813 β = 90 c = 117.395 γ = 90
Symmetry Space Group C 2 2 21
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 4 2003-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.0500 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.7 58.7 98.6 0.104 12.2 9.82 8940 8940 40
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.83 99.5 0.252 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 RdmB+SAM complex 2.7 58.72 8521 419 97.99 0.23059 0.22742 0.2398 0.29513 0.3048 RANDOM 32.176
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] -1.42 2.08 -0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.616 r_scangle_it 1.852 r_angle_refined_deg 1.201 r_scbond_it 0.989 r_mcangle_it 0.973 r_angle_other_deg 0.818 r_mcbond_it 0.511 r_symmetry_vdw_other 0.263 r_nbd_other 0.226 r_symmetry_vdw_refined 0.215
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.616 r_scangle_it 1.852 r_angle_refined_deg 1.201 r_scbond_it 0.989 r_mcangle_it 0.973 r_angle_other_deg 0.818 r_mcbond_it 0.511 r_symmetry_vdw_other 0.263 r_nbd_other 0.226 r_symmetry_vdw_refined 0.215 r_nbd_refined 0.204 r_symmetry_hbond_refined 0.19 r_xyhbond_nbd_refined 0.148 r_nbtor_other 0.081 r_chiral_restr 0.059 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2570 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 31
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement CCP4 data scaling