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Complex crystal structure of sp-Aspartate-Semialdehyde-Dehydrogenase with 3-carboxy-ethyl-phthalic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4R3N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295 15-22% PEG 3350, 0.1 M Na-acetate, 0.1 M MES (pH 6.5), 10 mM TCEP, 3% Ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.31 46.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.537 α = 90 b = 98.806 β = 101.16 c = 64.098 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 MARMOSAIC 300 mm CCD double crystal monochromator and K-B pair of biomorph mirrors 2014-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.033 APS 23-ID-D
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 1.8 50 99 0.12 26 4.6 66237 65575 1 2 29.5
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 1.81 1.87 97.3 0.808 4.4 6404
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 4R3N 1.81 50 2 65575 62262 3303 98.68 0.18565 0.18377 0.1918 0.21946 0.225 RANDOM 38.715
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] 1.1 2.05 1.56 -3.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.096 r_dihedral_angle_4_deg 19.531 r_dihedral_angle_3_deg 13.021 r_dihedral_angle_1_deg 5.972 r_long_range_B_refined 5.024 r_long_range_B_other 5.024 r_scangle_other 3.717 r_mcangle_it 2.562 r_mcangle_other 2.562 r_scbond_it 2.401
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.096 r_dihedral_angle_4_deg 19.531 r_dihedral_angle_3_deg 13.021 r_dihedral_angle_1_deg 5.972 r_long_range_B_refined 5.024 r_long_range_B_other 5.024 r_scangle_other 3.717 r_mcangle_it 2.562 r_mcangle_other 2.562 r_scbond_it 2.401 r_scbond_other 2.4 r_mcbond_it 1.829 r_mcbond_other 1.826 r_angle_refined_deg 1.377 r_angle_other_deg 0.745 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5448 Nucleic Acid Atoms Solvent Atoms 262 Heterogen Atoms 172
Software Software Software Name Purpose HKL-2000 data collection REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling