☰ Navigation Tabs
Crystal structure of tagatose-1,6-bisphosphate aldolase from Streptococcus pyogenes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MYP PDB ENTRY 3MYP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 287 0.1M sodium citrate, 0.1M MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 287K
Crystal Properties Matthews coefficient Solvent content 3.98 69.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.149 α = 90 b = 126.149 β = 90 c = 148.701 γ = 90
Symmetry Space Group P 43 21 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 ADSC QUANTUM 210 2009-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 6C1 1.2399 PAL/PLS 6C1
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 2.5 20 0.096 23.7 8.1 42128 32.6
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) 2.5 2.59 100 0.336 6.1 8.1 4155
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 3MYP 2.5 19.98 39947 2130 99.96 0.20136 0.20005 0.1983 0.2257 0.2246 RANDOM 22.794
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] 0.42 0.42 -0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.154 r_dihedral_angle_4_deg 21.282 r_dihedral_angle_3_deg 16.559 r_dihedral_angle_1_deg 5.695 r_scangle_it 2.701 r_scbond_it 1.506 r_angle_refined_deg 1.152 r_mcangle_it 1.01 r_mcbond_it 0.511 r_chiral_restr 0.081
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.154 r_dihedral_angle_4_deg 21.282 r_dihedral_angle_3_deg 16.559 r_dihedral_angle_1_deg 5.695 r_scangle_it 2.701 r_scbond_it 1.506 r_angle_refined_deg 1.152 r_mcangle_it 1.01 r_mcbond_it 0.511 r_chiral_restr 0.081 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5132 Nucleic Acid Atoms Solvent Atoms 192 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling