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The crystal structure of RibD from Escherichia coli in complex with the oxidised NADP+ cofactor in 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 20mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) at pH 7.4, 150mM NaCl, 10mM mercaptoethanol, 10% (v/v) glycerol, 2mM EDTA, 0.1M MES pH 6.5, 3% (v/v) 1,6 Hexandiol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.96 68.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 173 α = 90 b = 173 β = 90 c = 77.8 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 315 2005-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.2836 ESRF ID29
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 0.084 0.084 15.6 8.5 27098 27042 -3 -3 84
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 3.1 100 0.506 0.506 2.5 8.6 2514
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 28.93 27057 25679 1359 99.93 0.21496 0.21496 0.2122 0.2349 0.26653 0.2763 RANDOM 85.21
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] -1.03 -0.52 -1.03 1.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.876 r_dihedral_angle_3_deg 23.211 r_dihedral_angle_4_deg 21.071 r_dihedral_angle_1_deg 7.367 r_scangle_it 3.044 r_scbond_it 1.823 r_angle_refined_deg 1.784 r_mcangle_it 1.387 r_mcbond_it 0.866 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.876 r_dihedral_angle_3_deg 23.211 r_dihedral_angle_4_deg 21.071 r_dihedral_angle_1_deg 7.367 r_scangle_it 3.044 r_scbond_it 1.823 r_angle_refined_deg 1.784 r_mcangle_it 1.387 r_mcbond_it 0.866 r_nbtor_refined 0.317 r_nbd_refined 0.247 r_symmetry_vdw_refined 0.213 r_xyhbond_nbd_refined 0.183 r_symmetry_hbond_refined 0.147 r_chiral_restr 0.111 r_bond_refined_d 0.017 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5427 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement ADSC data collection XDS data reduction XSCALE data scaling MOLREP phasing