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Crystal Structure of 7,8-Diaminopelargonic Acid Synthase in complex with the trans-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 2.07 40.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.034 α = 90 b = 55.96 β = 109.65 c = 116.001 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 2001-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 0.991 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 2.15 22.36 98.6 0.066 13.9 41748 41748 31.2
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 2.15 2.27 96 0.291 2.9
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.15 22.36 39635 39635 2108 98.5 0.207 0.207 0.20465 0.2107 0.24028 0.2446 RANDOM 32.347
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] -2.28 -2.69 2.67 -2.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.55 r_dihedral_angle_1_deg 3.937 r_scangle_it 2.917 r_angle_other_deg 1.898 r_scbond_it 1.795 r_angle_refined_deg 1.583 r_mcangle_it 1.26 r_mcbond_it 0.677 r_symmetry_hbond_refined 0.401 r_nbtor_other 0.289
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.55 r_dihedral_angle_1_deg 3.937 r_scangle_it 2.917 r_angle_other_deg 1.898 r_scbond_it 1.795 r_angle_refined_deg 1.583 r_mcangle_it 1.26 r_mcbond_it 0.677 r_symmetry_hbond_refined 0.401 r_nbtor_other 0.289 r_nbd_refined 0.273 r_symmetry_vdw_refined 0.25 r_symmetry_vdw_other 0.245 r_nbd_other 0.221 r_xyhbond_nbd_other 0.178 r_xyhbond_nbd_refined 0.174 r_chiral_restr 0.092 r_gen_planes_other 0.026 r_bond_refined_d 0.016 r_gen_planes_refined 0.012 r_bond_other_d 0.004 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 6587 Nucleic Acid Atoms Solvent Atoms 324 Heterogen Atoms 60
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling AMoRE phasing REFMAC refinement CCP4 data scaling