☰ Navigation Tabs
Crystal Structure of Aspartate beta-Semialdehide Dehydrogenase from Streptococcus pneumoniae with 2',5'-Adenosine diphosphate and D-2-aminoadipate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GZ2 PDB ENTRY 2GZ2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 22% PEG 3350, 0.1M MES, 0.1 M ammonium acetate, 10 mM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.36 47.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.872 α = 90 b = 99.66 β = 100.91 c = 64.436 γ = 90
Symmetry Space Group P 1 21 1
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 MAR scanner 300 mm plate 2010-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.03 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.5 50 86.6 0.034 22.4 2.8 102882
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.55 43.9 0.18 5.1 2.1
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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 2GZ2 1.5 50 97679 5174 86.68 0.13173 0.13022 0.1288 0.15978 0.1604 RANDOM 16.623
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] -0.08 -0.06 0.58 -0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.504 r_dihedral_angle_4_deg 20.056 r_dihedral_angle_3_deg 11.682 r_dihedral_angle_1_deg 5.999 r_scangle_it 4.373 r_scbond_it 2.859 r_mcangle_it 1.812 r_angle_refined_deg 1.387 r_rigid_bond_restr 1.22 r_mcbond_it 1.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.504 r_dihedral_angle_4_deg 20.056 r_dihedral_angle_3_deg 11.682 r_dihedral_angle_1_deg 5.999 r_scangle_it 4.373 r_scbond_it 2.859 r_mcangle_it 1.812 r_angle_refined_deg 1.387 r_rigid_bond_restr 1.22 r_mcbond_it 1.072 r_chiral_restr 0.088 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5465 Nucleic Acid Atoms Solvent Atoms 769 Heterogen Atoms 112
Software Software Software Name Purpose Blu-Ice data collection REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling