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The crystal structure of glyceraldehyde-3-phosphate dehydrogenase from Bacillus anthracis str. Sterne
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CMC PDB ENTRY 3CMC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 0.2 M lithium sulfate, 25.5% PEG3350, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.31 46.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.347 α = 90.32 b = 102.044 β = 73.99 c = 102.144 γ = 68.99
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 315r mirrors 2011-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9794 APS 19-ID
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 2.55 40 97.2 0.06 13.8 2.1 90350 87718 1.7 1.7 45
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.55 2.59 89.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3CMC 2.55 40 69520 66018 3500 76.81 0.213 0.20796 0.2077 0.2696 0.2706 RANDOM 26.473
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] 1.02 -0.28 0.29 -0.5 -0.2 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.381 r_dihedral_angle_3_deg 20.994 r_dihedral_angle_4_deg 20.164 r_dihedral_angle_1_deg 6.701 r_angle_other_deg 2.613 r_angle_refined_deg 1.492 r_chiral_restr 0.076 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.381 r_dihedral_angle_3_deg 20.994 r_dihedral_angle_4_deg 20.164 r_dihedral_angle_1_deg 6.701 r_angle_other_deg 2.613 r_angle_refined_deg 1.492 r_chiral_restr 0.076 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.002 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_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19171 Nucleic Acid Atoms Solvent Atoms 258 Heterogen Atoms 35
Software Software Software Name Purpose SBC-Collect data collection MOLREP phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling