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Crystal complex structure of sp-Aspartate-Semialdehyde-Dehydrogenase with Nicotinamide Adenine dinucleotide phosphate and phthalic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PWK
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), 10mM TCEP, 3% Ethylene Glycol, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.29 46.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.78 α = 90 b = 98.399 β = 102.65 c = 63.973 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 2013-07-29 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 98.8 0.151 7.8 3 65690 64905 2 23.4
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 1.8 1.86 98.7 0.528 2.4 2.7 6446
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 3PWK 1.81 50 2 61525 3283 98.06 0.17689 0.17575 0.19775 0.2283 RANDOM 25.955
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] 0.53 0.98 -1.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.524 r_dihedral_angle_4_deg 17.974 r_dihedral_angle_3_deg 13.115 r_dihedral_angle_1_deg 5.827 r_long_range_B_refined 4.16 r_long_range_B_other 4.074 r_scangle_other 2.663 r_mcangle_it 1.762 r_mcangle_other 1.762 r_scbond_it 1.643
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.524 r_dihedral_angle_4_deg 17.974 r_dihedral_angle_3_deg 13.115 r_dihedral_angle_1_deg 5.827 r_long_range_B_refined 4.16 r_long_range_B_other 4.074 r_scangle_other 2.663 r_mcangle_it 1.762 r_mcangle_other 1.762 r_scbond_it 1.643 r_scbond_other 1.643 r_angle_refined_deg 1.281 r_mcbond_it 1.096 r_mcbond_other 1.095 r_angle_other_deg 0.746 r_chiral_restr 0.07 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5388 Nucleic Acid Atoms Solvent Atoms 287 Heterogen Atoms 155
Software Software Software Name Purpose HKL-2000 data collection REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling