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MAMMALIAN ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE: WILD-TYPE, ADDUCT WITH CYANOETHYL
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BBY PDB ENTRY 4BBY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 CRYSTALS WERE OBTAINED USING VAPOR-DIFFUSION SITTING-DROP AT 20 DEGREES C BY MIXING EQUAL VOLUMES OF 10 MG PROTEIN/ML IN 50 MM NACL, 5% (V/V) GLYCEROL, 50 MM TRIS/HCL PH 8.0 AND OF 30% (W/V) PEG1500 IN 100 MM NA/HEPES PH 7.5.
Crystal Properties Matthews coefficient Solvent content 2.18 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.91 α = 90.92 b = 98.62 β = 89.84 c = 106.28 γ = 95.66
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA SLS X06DA
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 2.4 54 97.7 0.12 8.9 4.2 92832
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 2.4 2.5 97 0.58 2.4 4.1
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 4BBY 2.41 54.06 91818 1014 97.58 0.18695 0.18627 0.1872 0.24767 0.2483 RANDOM 34.209
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] -1.61 -0.11 -0.62 -1.51 0.55 3.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.48 r_dihedral_angle_4_deg 19.077 r_dihedral_angle_3_deg 18.561 r_dihedral_angle_1_deg 6.633 r_angle_refined_deg 1.65 r_chiral_restr 0.105 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.48 r_dihedral_angle_4_deg 19.077 r_dihedral_angle_3_deg 18.561 r_dihedral_angle_1_deg 6.633 r_angle_refined_deg 1.65 r_chiral_restr 0.105 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17260 Nucleic Acid Atoms Solvent Atoms 320 Heterogen Atoms 243
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing