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Crystal Structure of the R391A Mutant of 7,8-Diaminopelargonic Acid Synthase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other WT dimer
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 294 PEG4000, MPD, HEPES, isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.06 40.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.88 α = 90 b = 55.899 β = 110.06 c = 116.237 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 2001-09-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 1.12 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 2.1 20.08 99.2 0.068 15.8 44984 44984 29.4
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 2.1 2.21 97.2 0.168 5.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 WT dimer 2.1 20.08 42715 42715 2269 0.2031 0.2031 0.2014 0.2086 0.2334 0.2334 RANDOM 32.259
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] -0.06 -0.09 -0.03 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.966 r_dihedral_angle_1_deg 4.011 r_scangle_it 2.848 r_scbond_it 1.724 r_angle_refined_deg 1.458 r_mcangle_it 1.269 r_angle_other_deg 1.225 r_symmetry_hbond_refined 0.754 r_mcbond_it 0.686 r_nbtor_other 0.611
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.966 r_dihedral_angle_1_deg 4.011 r_scangle_it 2.848 r_scbond_it 1.724 r_angle_refined_deg 1.458 r_mcangle_it 1.269 r_angle_other_deg 1.225 r_symmetry_hbond_refined 0.754 r_mcbond_it 0.686 r_nbtor_other 0.611 r_symmetry_vdw_other 0.282 r_nbd_refined 0.264 r_symmetry_vdw_refined 0.247 r_nbd_other 0.223 r_xyhbond_nbd_refined 0.2 r_xyhbond_nbd_other 0.118 r_chiral_restr 0.082 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6584 Nucleic Acid Atoms Solvent Atoms 342 Heterogen Atoms 48
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling AMoRE phasing REFMAC refinement CCP4 data scaling