☰ Navigation Tabs
Crystal Structure of the dTDP-4-dehydrorhamnose Reductase from Streptococcus pneumoniae.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WPG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.3 292 Protein: 3.3 mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3;
Screen: PEG's II (H1), 0.01M tri-Sodium citrate, 33% (w/v) PEG6000;
Crystal Properties Matthews coefficient Solvent content 2.05 39.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.178 α = 90 b = 120.178 β = 90 c = 48.075 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 9M 2021-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.77482 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 30 99.1 0.07 0.07 0.074 0.025 0.997 28 8 138569 -3 17.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1 1.02 98.3 1.207 1.207 0.456 0.502 1.9 7.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1 22.72 131576 6992 99.06 0.12632 0.12543 0.133 0.14319 0.1502 RANDOM 12.486
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] 0.27 0.13 0.27 -0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 9.825 r_dihedral_angle_1_deg 5.13 r_rigid_bond_restr 4.999 r_dihedral_angle_2_deg 3.506 r_long_range_B_refined 3.265 r_long_range_B_other 2.151 r_scangle_other 1.182 r_angle_refined_deg 1.146 r_mcangle_it 1.077 r_mcangle_other 1.077
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 9.825 r_dihedral_angle_1_deg 5.13 r_rigid_bond_restr 4.999 r_dihedral_angle_2_deg 3.506 r_long_range_B_refined 3.265 r_long_range_B_other 2.151 r_scangle_other 1.182 r_angle_refined_deg 1.146 r_mcangle_it 1.077 r_mcangle_other 1.077 r_scbond_it 0.812 r_scbond_other 0.811 r_mcbond_it 0.69 r_mcbond_other 0.69 r_angle_other_deg 0.373 r_chiral_restr 0.058 r_gen_planes_refined 0.015 r_gen_planes_other 0.013 r_bond_refined_d 0.004 r_bond_other_d 0.001 r_dihedral_angle_4_deg 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_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2299 Nucleic Acid Atoms Solvent Atoms 529 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling PHASER phasing