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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 NADPH prior to data collection., VAPOR DIFFUSION, SITTING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 3.08 60.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 169.332 α = 90 b = 81.601 β = 104.11 c = 98.384 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 ADSC QUANTUM 4 2006-04-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X26C 1.10 NSLS X26C
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 2.26 50 99.2 0.058 23.1 4 61088 60599
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 2.26 2.34 93.2 0.24 5.5 3.6 5651
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 3CGC 2.262 42.11 57783 57517 3078 99.54 0.17884 0.17701 0.1737 0.21371 0.2078 RANDOM 57.562
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] -2.65 -0.17 5.4 -2.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.268 r_dihedral_angle_4_deg 15.653 r_dihedral_angle_3_deg 14.254 r_dihedral_angle_1_deg 5.68 r_scangle_it 1.963 r_scbond_it 1.159 r_angle_refined_deg 1.155 r_mcangle_it 0.744 r_mcbond_it 0.434 r_nbtor_refined 0.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.268 r_dihedral_angle_4_deg 15.653 r_dihedral_angle_3_deg 14.254 r_dihedral_angle_1_deg 5.68 r_scangle_it 1.963 r_scbond_it 1.159 r_angle_refined_deg 1.155 r_mcangle_it 0.744 r_mcbond_it 0.434 r_nbtor_refined 0.296 r_nbd_refined 0.184 r_symmetry_vdw_refined 0.15 r_symmetry_hbond_refined 0.118 r_xyhbond_nbd_refined 0.111 r_chiral_restr 0.075 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6958 Nucleic Acid Atoms Solvent Atoms 391 Heterogen Atoms 298
Software Software Software Name Purpose REFMAC refinement CBASS data collection HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing