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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 3CGB PDB ENTRY 3CGB
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)+, VAPOR DIFFUSION, SITTING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 3.09 60.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 169.526 α = 90 b = 81.74 β = 103.97 c = 98.37 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 2005-09-29 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 2.3 25.61 99.9 0.095 19.8 6.6 58130 58072
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 2.3 2.42 100 0.279 6 6.4 8452
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 3CGB 2.3 25.11 55133 55094 2949 99.93 0.19403 0.19171 0.1942 0.2375 0.2407 RANDOM 23.1
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.865 r_dihedral_angle_4_deg 17.185 r_dihedral_angle_3_deg 14.531 r_dihedral_angle_1_deg 5.811 r_scangle_it 1.885 r_angle_refined_deg 1.141 r_scbond_it 1.109 r_mcangle_it 0.878 r_mcbond_it 0.501 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.865 r_dihedral_angle_4_deg 17.185 r_dihedral_angle_3_deg 14.531 r_dihedral_angle_1_deg 5.811 r_scangle_it 1.885 r_angle_refined_deg 1.141 r_scbond_it 1.109 r_mcangle_it 0.878 r_mcbond_it 0.501 r_nbtor_refined 0.299 r_symmetry_vdw_refined 0.197 r_nbd_refined 0.191 r_symmetry_hbond_refined 0.115 r_xyhbond_nbd_refined 0.109 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6958 Nucleic Acid Atoms Solvent Atoms 442 Heterogen Atoms 202
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection MOSFLM data reduction SCALA data scaling REFMAC phasing