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Pyridine Nucleotide Complexes with Bacillus anthracis Coenzyme A-Disulfide Reductase: A Structural Analysis of Dual NAD(P)H Specificity
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CGC PDB ENTRY 3CGC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 288 16-26% 2-methyl-2,4-pentanediol, 0.2 M magnesium acetate, 0.1 M sodium cacodylate, pH 6.5, and 2 mM NAD(P)+. Crystal soaked in NADH prior to data collection., VAPOR DIFFUSION, SITTING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 3.06 59.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 169.612 α = 90 b = 81.171 β = 104.01 c = 98.052 γ = 90
Symmetry Space Group C 1 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 RIGAKU SATURN 92 Confocal Blue Max-Flux 2006-02-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 2.25 38.14 97.2 0.081 7.8 3.8 61451 59708
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) 1 2.25 2.33 96.1 0.24 3.5 3.78 6088
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3CGC 2.25 37.45 58321 56006 3006 96.03 0.20798 0.20589 0.24782 0.3078 RANDOM 47.844
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] 0.16 0.08 -0.36 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.503 r_dihedral_angle_4_deg 17.632 r_dihedral_angle_3_deg 15.35 r_dihedral_angle_1_deg 5.978 r_scangle_it 2.099 r_scbond_it 1.273 r_angle_refined_deg 1.263 r_mcangle_it 0.774 r_mcbond_it 0.445 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.503 r_dihedral_angle_4_deg 17.632 r_dihedral_angle_3_deg 15.35 r_dihedral_angle_1_deg 5.978 r_scangle_it 2.099 r_scbond_it 1.273 r_angle_refined_deg 1.263 r_mcangle_it 0.774 r_mcbond_it 0.445 r_nbtor_refined 0.3 r_nbd_refined 0.194 r_symmetry_vdw_refined 0.176 r_xyhbond_nbd_refined 0.131 r_symmetry_hbond_refined 0.129 r_chiral_restr 0.082 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6958 Nucleic Acid Atoms Solvent Atoms 460 Heterogen Atoms 290
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection d*TREK data reduction d*TREK data scaling REFMAC phasing