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Structure of Aspartate Semialdehyde Dehydrogenase (ASADH) from Streptococcus pneumoniae complexed with NADP and aspartate-semialdehyde
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GZ1 PDB Entry: 2GZ1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 50 mM Citrate pH 6.0
200 mM ammonium acetate
20% PEG 8000
10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.32 46.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.348 α = 89.98 b = 64.439 β = 81.06 c = 96.739 γ = 82
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 2006-01-15 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 2.3 43.58 92.7 0.113 6.6 3.3 95735 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 2.3 2.38 89.6 0.293 3.3 3.31 5581
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: 2GZ1 2.1 30.01 75010 75010 3769 91.68 0.214 0.214 0.211 0.2106 0.277 0.274 RANDOM 22.018
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] 0.27 -0.03 -0.04 -0.01 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.697 r_dihedral_angle_4_deg 17.199 r_dihedral_angle_3_deg 16.158 r_dihedral_angle_1_deg 6.103 r_scangle_it 2.285 r_scbond_it 1.444 r_angle_refined_deg 1.334 r_mcangle_it 0.846 r_mcbond_it 0.511 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.697 r_dihedral_angle_4_deg 17.199 r_dihedral_angle_3_deg 16.158 r_dihedral_angle_1_deg 6.103 r_scangle_it 2.285 r_scbond_it 1.444 r_angle_refined_deg 1.334 r_mcangle_it 0.846 r_mcbond_it 0.511 r_nbtor_refined 0.3 r_nbd_refined 0.197 r_symmetry_vdw_refined 0.162 r_xyhbond_nbd_refined 0.157 r_symmetry_hbond_refined 0.145 r_chiral_restr 0.086 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10759 Nucleic Acid Atoms Solvent Atoms 808 Heterogen Atoms 224
Software Software Software Name Purpose d*TREK data scaling REFMAC refinement PDB_EXTRACT data extraction CrystalClear data reduction PHASER phasing