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Human brain aspartoacylase mutant Y231C 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
Crystal Properties Matthews coefficient Solvent content 3.96 68.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 147.959 α = 90 b = 147.959 β = 90 c = 103.456 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 2014-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.283 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 2.9 50 100 0.142 10.7 4.7 25970
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 2.9 3 99.9 0.74 2.1 4.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2O4H 2.9 48.88 24598 1320 99.64 0.19913 0.19724 0.1979 0.23473 0.2271 RANDOM 70.51
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] 1.59 1.59 -3.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.72 r_dihedral_angle_3_deg 17.501 r_dihedral_angle_4_deg 17.28 r_long_range_B_refined 8.744 r_long_range_B_other 8.743 r_scangle_other 6.207 r_mcangle_it 6.106 r_mcangle_other 6.104 r_dihedral_angle_1_deg 6.074 r_mcbond_it 3.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.72 r_dihedral_angle_3_deg 17.501 r_dihedral_angle_4_deg 17.28 r_long_range_B_refined 8.744 r_long_range_B_other 8.743 r_scangle_other 6.207 r_mcangle_it 6.106 r_mcangle_other 6.104 r_dihedral_angle_1_deg 6.074 r_mcbond_it 3.94 r_mcbond_other 3.94 r_scbond_it 3.817 r_scbond_other 3.816 r_angle_refined_deg 1.299 r_angle_other_deg 0.879 r_chiral_restr 0.066 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.003 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4830 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement