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Crystal Structure of the R253K 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 PEG4000, MPD, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 100K
Crystal Properties Matthews coefficient Solvent content 2.08 40.76
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 2002-09-14 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 2.2 20 99.2 0.124 11 3.5 39945 39626 26.9
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) 2.2 2.32 98.2 0.421 2.4 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 FOURIER SYNTHESIS THROUGHOUT WT dimer 2.2 20 37212 37212 2010 98.21 0.193 0.19327 0.191 0.22567 0.2109 RANDOM 25.122
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] -0.31 0.6 3.3 -2.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.25 r_dihedral_angle_1_deg 3.824 r_scangle_it 2.955 r_scbond_it 1.739 r_angle_refined_deg 1.592 r_angle_other_deg 1.183 r_mcangle_it 1.075 r_mcbond_it 0.573 r_symmetry_hbond_other 0.503 r_symmetry_hbond_refined 0.497
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.25 r_dihedral_angle_1_deg 3.824 r_scangle_it 2.955 r_scbond_it 1.739 r_angle_refined_deg 1.592 r_angle_other_deg 1.183 r_mcangle_it 1.075 r_mcbond_it 0.573 r_symmetry_hbond_other 0.503 r_symmetry_hbond_refined 0.497 r_symmetry_vdw_other 0.468 r_symmetry_vdw_refined 0.416 r_nbtor_other 0.298 r_nbd_refined 0.268 r_nbd_other 0.212 r_xyhbond_nbd_refined 0.156 r_xyhbond_nbd_other 0.1 r_chiral_restr 0.084 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6666 Nucleic Acid Atoms Solvent Atoms 336 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling SFALL phasing