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Crystal Structure of 7,8-Diaminopelargonic Acid Synthase in complex with the cis isomer of amiclenomycin
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 294 PEG4000, MPD, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.08 40.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.655 α = 90 b = 56.073 β = 109.86 c = 116.174 γ = 90
Symmetry Space Group C 1 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 MARRESEARCH 2001-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 0.968 MAX II I711
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 1.81 40.16 99 0.062 17.4 70391 70391 23.1
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 1.81 1.91 94.1 0.259 3.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.81 20 66847 66847 3492 99.9 0.19572 0.19572 0.19439 0.22045 0.2288 RANDOM 23.278
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] -1.08 -1.24 1.57 -1.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.172 r_dihedral_angle_1_deg 3.86 r_scangle_it 2.29 r_scbond_it 1.403 r_angle_refined_deg 1.376 r_angle_other_deg 1.177 r_mcangle_it 0.999 r_mcbond_it 0.542 r_symmetry_hbond_refined 0.301 r_nbd_refined 0.266
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.172 r_dihedral_angle_1_deg 3.86 r_scangle_it 2.29 r_scbond_it 1.403 r_angle_refined_deg 1.376 r_angle_other_deg 1.177 r_mcangle_it 0.999 r_mcbond_it 0.542 r_symmetry_hbond_refined 0.301 r_nbd_refined 0.266 r_symmetry_vdw_refined 0.257 r_xyhbond_nbd_other 0.255 r_symmetry_vdw_other 0.241 r_nbd_other 0.214 r_xyhbond_nbd_refined 0.186 r_nbtor_other 0.129 r_chiral_restr 0.09 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_gen_planes_other 0.003 r_bond_other_d 0.001 r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6588 Nucleic Acid Atoms Solvent Atoms 537 Heterogen Atoms 60
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling AMoRE phasing REFMAC refinement CCP4 data scaling