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Human brain aspartoacylase mutant E285A complex with intermediate analog (N-phosphonomethyl-L-aspartate)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O4H PDB Entry 2o4h
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 277 14% PEG 3350, 0.05M sodium citrate, 0.3M potassium phosphate (dibasic), 3% ethylene glycol, 0.01M DTT, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.92 68.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 147.736 α = 90 b = 147.736 β = 90 c = 102.738 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 mirrors 2013-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.97934 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 3 50 90 0.101 9.4 2.6 17286 2 2 49.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.11 90 0.188 3 1.3 377
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB Entry 2o4h 3 46.76 2 39582 16360 886 73.79 0.19344 0.19089 0.24052 0.2257 RANDOM 72.212
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] 3.64 3.64 -7.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.696 r_dihedral_angle_4_deg 22.948 r_dihedral_angle_3_deg 18.245 r_long_range_B_refined 8.661 r_long_range_B_other 8.627 r_dihedral_angle_1_deg 5.899 r_scangle_other 5.538 r_mcangle_it 5.387 r_mcangle_other 5.381 r_mcbond_it 3.281
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.696 r_dihedral_angle_4_deg 22.948 r_dihedral_angle_3_deg 18.245 r_long_range_B_refined 8.661 r_long_range_B_other 8.627 r_dihedral_angle_1_deg 5.899 r_scangle_other 5.538 r_mcangle_it 5.387 r_mcangle_other 5.381 r_mcbond_it 3.281 r_mcbond_other 3.28 r_scbond_it 3.241 r_scbond_other 3.24 r_angle_refined_deg 1.148 r_angle_other_deg 0.897 r_chiral_restr 0.062 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4834 Nucleic Acid Atoms Solvent Atoms 33 Heterogen Atoms 28
Software Software Software Name Purpose Blu-Ice data collection CCP4 model building REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling CCP4 phasing