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Crystal structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase from Yersinia pestis CO92
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1G57
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 302 0.2 M Lithium Sulfate,
0.1M Tris pH 8.5,
25% Peg3350, VAPOR DIFFUSION, SITTING DROP, temperature 302K
Crystal Properties Matthews coefficient Solvent content 1.86 33.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.907 α = 90 b = 70.815 β = 90.13 c = 62.297 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 CCD SBC-3 mirrors 2008-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.9794 APS 19-BM
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 1.9 33.64 99.3 0.066 17.4 3.2 27680 27484 2 2
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 1.9 1.95 99.8 0.35 4.2 3.2
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1G57 1.95 33.64 25180 24366 802 99.23 0.2007 0.19893 0.25321 0.2654 RANDOM 12.253
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] 1.96 -0.36 -0.62 -1.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.105 r_dihedral_angle_3_deg 15.388 r_dihedral_angle_4_deg 15.381 r_dihedral_angle_1_deg 6.806 r_scangle_it 3.404 r_scbond_it 2.217 r_angle_refined_deg 1.699 r_angle_other_deg 1.461 r_mcangle_it 1.285 r_mcbond_it 0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.105 r_dihedral_angle_3_deg 15.388 r_dihedral_angle_4_deg 15.381 r_dihedral_angle_1_deg 6.806 r_scangle_it 3.404 r_scbond_it 2.217 r_angle_refined_deg 1.699 r_angle_other_deg 1.461 r_mcangle_it 1.285 r_mcbond_it 0.83 r_mcbond_other 0.212 r_chiral_restr 0.1 r_bond_refined_d 0.02 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3069 Nucleic Acid Atoms Solvent Atoms 158 Heterogen Atoms
Software Software Software Name Purpose SBC-Collect data collection MOLREP phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling