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Crystal Structure of the D147N Mutant of 7,8-Diaminopelargonic Acid Synthase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other wild-type dimer
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 40.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.08 α = 90 b = 56.527 β = 96.32 c = 120.993 γ = 90
Symmetry Space Group P 1 21 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 2002-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 1.10 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 99.7 0.089 11.8 3.3 48622 26.7
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) 2.1 2.21 99.2 0.331 2.9 3.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT wild-type dimer 2.1 20 44599 44599 2621 96.72 0.2029 0.20294 0.20161 0.22728 0.2157 RANDOM 28.356
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] -1.31 0.74 3.41 -1.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.243 r_dihedral_angle_1_deg 3.909 r_scangle_it 2.741 r_scbond_it 1.677 r_angle_refined_deg 1.607 r_angle_other_deg 1.6 r_mcangle_it 1.195 r_mcbond_it 0.645 r_symmetry_hbond_refined 0.463 r_symmetry_vdw_other 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.243 r_dihedral_angle_1_deg 3.909 r_scangle_it 2.741 r_scbond_it 1.677 r_angle_refined_deg 1.607 r_angle_other_deg 1.6 r_mcangle_it 1.195 r_mcbond_it 0.645 r_symmetry_hbond_refined 0.463 r_symmetry_vdw_other 0.315 r_symmetry_vdw_refined 0.297 r_nbd_refined 0.261 r_nbd_other 0.218 r_xyhbond_nbd_other 0.212 r_xyhbond_nbd_refined 0.193 r_nbtor_other 0.18 r_chiral_restr 0.108 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_gen_planes_other 0.005 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6436 Nucleic Acid Atoms Solvent Atoms 402 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling AMoRE phasing