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Crystal Structure of the R253A 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 2.09 41.12
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 IMAGE PLATE MARRESEARCH 2001-08-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B 0.85 EMBL/DESY, HAMBURG BW7B
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 2.42 20 90.6 0.077 14.8 29730 26936 34.7
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) 1 2.42 2.48 55.3 0.028 24.8
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 2.42 20 25407 25407 1413 89.32 0.19 0.18968 0.18776 0.1945 0.22414 0.2316 RANDOM 28.654
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] -1.2 0.48 2.59 -1.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.18 r_dihedral_angle_1_deg 3.93 r_scangle_it 3.201 r_scbond_it 1.883 r_angle_refined_deg 1.654 r_mcangle_it 1.316 r_angle_other_deg 1.174 r_mcbond_it 0.697 r_symmetry_vdw_refined 0.476 r_symmetry_vdw_other 0.462
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.18 r_dihedral_angle_1_deg 3.93 r_scangle_it 3.201 r_scbond_it 1.883 r_angle_refined_deg 1.654 r_mcangle_it 1.316 r_angle_other_deg 1.174 r_mcbond_it 0.697 r_symmetry_vdw_refined 0.476 r_symmetry_vdw_other 0.462 r_nbd_refined 0.276 r_nbtor_other 0.271 r_nbd_other 0.218 r_xyhbond_nbd_refined 0.171 r_symmetry_hbond_refined 0.128 r_xyhbond_nbd_other 0.126 r_chiral_restr 0.09 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6590 Nucleic Acid Atoms Solvent Atoms 243 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing