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Structure of aspartate semialdehyde dehydrogenase (ASADH) from Streptococcus pneumoniae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YS4 PDB Entry: 1YS4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 100 mM MES pH 6.5
50 mM calcium acetate
20% PEG 3350
10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.23 44.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.479 α = 90 b = 78.686 β = 90 c = 243.41 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV 2005-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU
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 2.1 29.12 94.6 0.085 8 3.27 77734 77734 2 2
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 2.1 2.18 99.9 0.254 3.9 3.5 8072
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 (All) 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: 1YS4 2.1 29.11 77719 77719 3948 94.58 0.18 0.18 0.178 0.1894 0.221 0.2327 RANDOM 12.421
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] 1.03 -0.7 -0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.965 r_scangle_it 1.825 r_angle_refined_deg 1.104 r_scbond_it 1.085 r_angle_other_deg 0.76 r_mcangle_it 0.578 r_mcbond_it 0.302 r_nbd_other 0.228 r_symmetry_vdw_other 0.227 r_symmetry_hbond_refined 0.189
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.965 r_scangle_it 1.825 r_angle_refined_deg 1.104 r_scbond_it 1.085 r_angle_other_deg 0.76 r_mcangle_it 0.578 r_mcbond_it 0.302 r_nbd_other 0.228 r_symmetry_vdw_other 0.227 r_symmetry_hbond_refined 0.189 r_nbd_refined 0.181 r_symmetry_vdw_refined 0.173 r_xyhbond_nbd_refined 0.152 r_nbtor_other 0.079 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10562 Nucleic Acid Atoms Solvent Atoms 1003 Heterogen Atoms
Software Software Software Name Purpose d*TREK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data reduction