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Human brain aspartoacylase mutant K213E 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 3.85 68.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.072 α = 90 b = 146.072 β = 90 c = 103.424 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 2.6 50 95 0.106 10.5 3.7 28127 2 2 36.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.69 95 0.206 0.206 3.1 1.5 1058
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 2o4h 2.6 46.25 2 2 28127 26625 1409 80.07 0.20088 0.1991 0.1934 0.23429 0.2261 RANDOM 53.376
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 -2.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.057 r_dihedral_angle_4_deg 16.683 r_dihedral_angle_3_deg 16.4 r_long_range_B_refined 6.176 r_long_range_B_other 6.176 r_dihedral_angle_1_deg 5.822 r_mcangle_it 3.973 r_scangle_other 3.973 r_mcangle_other 3.972 r_mcbond_it 2.432
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.057 r_dihedral_angle_4_deg 16.683 r_dihedral_angle_3_deg 16.4 r_long_range_B_refined 6.176 r_long_range_B_other 6.176 r_dihedral_angle_1_deg 5.822 r_mcangle_it 3.973 r_scangle_other 3.973 r_mcangle_other 3.972 r_mcbond_it 2.432 r_mcbond_other 2.431 r_scbond_it 2.288 r_scbond_other 2.285 r_angle_refined_deg 1.134 r_angle_other_deg 0.697 r_chiral_restr 0.059 r_bond_refined_d 0.007 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 4842 Nucleic Acid Atoms Solvent Atoms 67 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