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Crystal Structure of an Aspartate-Semialdehyde Dehydrogenase from Burkholderia Thailandensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MB4 PDB ENTRY 1MB4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 290 Internal tracking number 226078. Wizard 3/4 well F8. 0.1M MMT Buffer/NaOH pH 9.0, 25% w/v PEG1500, 20% Ethylene Glycol for Cryo. ButhA.17885.a.A1 PS01196 CR_24 58.0mg/ml., vapor diffusion, sitting drop, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.61 52.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.45 α = 90 b = 103.1 β = 90 c = 106.97 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 MAR scanner 300 mm plate 2011-10-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97586 APS 21-ID-G
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 1.55 47.48 99.9 0.058 19.05 7.4 123001 122928 -3 -3 24.061
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 1.55 1.59 100 0.421 4.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 1MB4 1.55 47.48 2 123001 122839 6174 99.94 0.152 0.152 0.151 0.1581 0.173 0.1784 RANDOM 18.7
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] -0.11 -0.11 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.821 r_dihedral_angle_4_deg 22.789 r_dihedral_angle_3_deg 11.209 r_dihedral_angle_1_deg 5.65 r_angle_refined_deg 1.427 r_angle_other_deg 0.925 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.821 r_dihedral_angle_4_deg 22.789 r_dihedral_angle_3_deg 11.209 r_dihedral_angle_1_deg 5.65 r_angle_refined_deg 1.427 r_angle_other_deg 0.925 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5547 Nucleic Acid Atoms Solvent Atoms 860 Heterogen Atoms 8
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MD2 data collection XDS data reduction