☰ Navigation Tabs
Human brain aspartoacylase complex with intermediate analog (N-phosphonomethyl-L-aspartate)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2I3C PDB entry 2I3C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 8-10 mg/ml Protein, 50 mM Sodium citrate pH 6.0, 300 mM K2HPO4, 15-19% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 3.74 67.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.081 α = 90 b = 143.081 β = 90 c = 104.604 γ = 90
Symmetry Space Group P 42 21 2
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 Kirkpatrick-Baez pair of focusing bimorph mirrors 2006-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.28300 APS 23-ID-B
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 2.7 50 95.3 0.094 20.7 10.7 28991 27490 72.7
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 2.7 2.8 62.7 0.354 2.9 5.3 1849
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 (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 PDB entry 2I3C 2.7 46.47 27490 27490 1449 95.23 0.20544 0.20211 0.19 0.27138 0.2549 RANDOM 59.981
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] 0.58 0.58 -1.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.018 r_dihedral_angle_3_deg 19.608 r_dihedral_angle_4_deg 10.473 r_dihedral_angle_1_deg 7.269 r_scangle_it 2.779 r_angle_refined_deg 1.639 r_scbond_it 1.639 r_mcangle_it 1.346 r_mcbond_it 0.748 r_nbtor_refined 0.318
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.018 r_dihedral_angle_3_deg 19.608 r_dihedral_angle_4_deg 10.473 r_dihedral_angle_1_deg 7.269 r_scangle_it 2.779 r_angle_refined_deg 1.639 r_scbond_it 1.639 r_mcangle_it 1.346 r_mcbond_it 0.748 r_nbtor_refined 0.318 r_nbd_refined 0.215 r_symmetry_vdw_refined 0.185 r_xyhbond_nbd_refined 0.145 r_chiral_restr 0.099 r_symmetry_hbond_refined 0.067 r_metal_ion_refined 0.042 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4842 Nucleic Acid Atoms Solvent Atoms 69 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection HKL-2000 data reduction SCALEPACK data scaling REFMAC phasing