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Crystal Structure of the Y17F 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 2.06 40.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.508 α = 90 b = 55.659 β = 97.04 c = 121.396 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 1.71 20 97.2 0.096 11.5 4 83943 81593 22
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) 1.71 1.8 90.7 0.408 2.6 3.9
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 wild-type dimer 1.71 19.92 77492 77492 4065 98.77 0.19 0.18692 0.18592 0.1977 0.20557 0.2164 RANDOM 21.231
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 0.44 1.74 -0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.39 r_dihedral_angle_1_deg 3.687 r_scangle_it 2.307 r_scbond_it 1.417 r_angle_refined_deg 1.362 r_angle_other_deg 1.155 r_mcangle_it 0.944 r_symmetry_hbond_refined 0.51 r_mcbond_it 0.509 r_symmetry_vdw_refined 0.402
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.39 r_dihedral_angle_1_deg 3.687 r_scangle_it 2.307 r_scbond_it 1.417 r_angle_refined_deg 1.362 r_angle_other_deg 1.155 r_mcangle_it 0.944 r_symmetry_hbond_refined 0.51 r_mcbond_it 0.509 r_symmetry_vdw_refined 0.402 r_symmetry_vdw_other 0.306 r_nbtor_other 0.303 r_nbd_refined 0.262 r_nbd_other 0.21 r_xyhbond_nbd_refined 0.168 r_xyhbond_nbd_other 0.092 r_chiral_restr 0.09 r_bond_refined_d 0.011 r_gen_planes_other 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6696 Nucleic Acid Atoms Solvent Atoms 660 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling AMoRE phasing