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Crystal structure of E. coli dihydrodipicolinate synthase with pyruvate and succinic semi-aldehyde bound in active site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YXC PDB ENTRY 1YXC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 10 277 6% w/v N-octyl-R-glucopyranoside, 1.8 M potassium phosphate dibasic, pH 10.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.69 66.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.172 α = 90 b = 121.172 β = 90 c = 109.732 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD ADSC QUANTUM 315r 2008-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 Australian Synchrotron MX2
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 29.1 89.11 0.103 4.8 37212 35072 1 1
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 2.359 90.79 0.325 4.7 2550
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 1YXC 2.3 29.1 37212 35072 2110 89.11 0.14646 0.14646 0.14344 0.1436 0.19779 0.1973 RANDOM 17.109
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] -0.14 -0.07 -0.14 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.21 r_dihedral_angle_4_deg 17.125 r_dihedral_angle_3_deg 15.778 r_dihedral_angle_1_deg 6.515 r_angle_refined_deg 1.94 r_chiral_restr 0.123 r_bond_refined_d 0.019 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4378 Nucleic Acid Atoms Solvent Atoms 459 Heterogen Atoms 16
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling