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Crystal Structure of the Y144F 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 2.04 39.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.353 α = 90 b = 55.513 β = 96.95 c = 120.727 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 2002-09-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 1.13 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 1.83 20 99.2 0.052 17.1 3.8 68200 67655 22.1
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) 1.83 1.93 94.8 0.216 5.2 3.6
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 FOURIER SYNTHESIS THROUGHOUT wild-type dimer 1.83 19.96 64168 64168 3411 99.95 0.183 0.18202 0.181 0.19 0.20493 0.2162 RANDOM 21.937
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] -1.19 0.36 2.13 -0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.811 r_dihedral_angle_1_deg 3.723 r_scangle_it 2.453 r_scbond_it 1.498 r_angle_refined_deg 1.355 r_angle_other_deg 1.075 r_mcangle_it 0.946 r_mcbond_it 0.502 r_symmetry_hbond_refined 0.392 r_symmetry_vdw_refined 0.278
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.811 r_dihedral_angle_1_deg 3.723 r_scangle_it 2.453 r_scbond_it 1.498 r_angle_refined_deg 1.355 r_angle_other_deg 1.075 r_mcangle_it 0.946 r_mcbond_it 0.502 r_symmetry_hbond_refined 0.392 r_symmetry_vdw_refined 0.278 r_symmetry_vdw_other 0.262 r_nbd_refined 0.261 r_nbd_other 0.209 r_xyhbond_nbd_refined 0.184 r_xyhbond_nbd_other 0.14 r_nbtor_other 0.106 r_chiral_restr 0.095 r_bond_refined_d 0.01 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 6672 Nucleic Acid Atoms Solvent Atoms 572 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling SFALL phasing