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MAMMALIAN ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE: Tyr578Phe mutant
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 2.26 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.68 α = 90.43 b = 99.32 β = 92.12 c = 107.98 γ = 95.2
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 MARESEARCH 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 48 98.6 0.16 8.8 4.4 98369
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 98 0.75 2.3 4.4
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 2.4 47.58 97288 1080 98.65 0.18816 0.18748 0.1903 0.2522 0.2504 RANDOM 28.18
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] 0.37 0.07 -0.51 -0.32 -0.39 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.651 r_dihedral_angle_4_deg 20.993 r_dihedral_angle_3_deg 18.908 r_dihedral_angle_1_deg 7.058 r_scangle_it 4.405 r_scbond_it 2.693 r_angle_refined_deg 1.812 r_mcangle_it 1.56 r_mcbond_it 0.808 r_chiral_restr 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.651 r_dihedral_angle_4_deg 20.993 r_dihedral_angle_3_deg 18.908 r_dihedral_angle_1_deg 7.058 r_scangle_it 4.405 r_scbond_it 2.693 r_angle_refined_deg 1.812 r_mcangle_it 1.56 r_mcbond_it 0.808 r_chiral_restr 0.12 r_bond_refined_d 0.019 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_other r_mcangle_other r_scbond_other 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 17446 Nucleic Acid Atoms Solvent Atoms 492 Heterogen Atoms 251
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing