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The crystal structure of RibD from Escherichia coli in complex with a substrate analogue, ribose 5-phosphate (beta form), bound to the active site of the reductase domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2G6V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.1M MES pH 6.5, 3% (v/v) 1,6 Hexandiol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.7 66.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 173.1 α = 90 b = 173.1 β = 90 c = 76.7 γ = 120
Symmetry Space Group P 31 2 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 ADSC QUANTUM 4 2004-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 3 30 99.8 0.081 0.081 17.2 4.9 26730 26665 -3 -3 59
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.1 99.1 0.409 0.409 3.8 4.8 2435
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 (All) 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 2G6V 3 28.86 26665 25319 1346 99.9 0.22502 0.22502 0.22227 0.2143 0.27557 0.2669 RANDOM 58.742
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] -0.33 -0.17 -0.33 0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.888 r_dihedral_angle_3_deg 20.43 r_dihedral_angle_4_deg 18.179 r_dihedral_angle_1_deg 6.877 r_scangle_it 1.837 r_angle_refined_deg 1.345 r_scbond_it 1.064 r_mcangle_it 0.847 r_mcbond_it 0.503 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.888 r_dihedral_angle_3_deg 20.43 r_dihedral_angle_4_deg 18.179 r_dihedral_angle_1_deg 6.877 r_scangle_it 1.837 r_angle_refined_deg 1.345 r_scbond_it 1.064 r_mcangle_it 0.847 r_mcbond_it 0.503 r_nbtor_refined 0.305 r_nbd_refined 0.232 r_symmetry_vdw_refined 0.207 r_xyhbond_nbd_refined 0.167 r_symmetry_hbond_refined 0.099 r_chiral_restr 0.089 r_bond_refined_d 0.009 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5472 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement ProDC data collection XDS data reduction XSCALE data scaling MOLREP phasing