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Crystal Structure of the CBS domains from the Bacillus subtilis CcpN repressor complexed with AppNp, phosphate and magnesium ions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FV6 PDB ENTRY 3FV6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 289 17% PEG 2000 MME, 0.1M HEPES, 8mg/ml Protein; Drops 1+1 microliter, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 1.92 35.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.025 α = 90 b = 103.969 β = 90 c = 98.387 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 78 CCD ADSC QUANTUM 315r 2006-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.97549 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 2.03 51.99 99.8 0.086 0.111 15.2 6.9 18288 26.233
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 2.03 2.14 100 0.417 0.417 3.9 7.1 17324
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 3FV6 2.03 29.17 17324 17324 934 99.77 0.19233 0.18875 0.2034 0.26203 0.2702 RANDOM 30.269
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] -0.56 0.75 -0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.627 r_dihedral_angle_3_deg 18.16 r_dihedral_angle_4_deg 14.746 r_dihedral_angle_1_deg 7.401 r_scangle_it 5.132 r_scbond_it 3.349 r_angle_refined_deg 2.366 r_mcangle_it 1.941 r_mcbond_it 1.145 r_chiral_restr 0.202
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.627 r_dihedral_angle_3_deg 18.16 r_dihedral_angle_4_deg 14.746 r_dihedral_angle_1_deg 7.401 r_scangle_it 5.132 r_scbond_it 3.349 r_angle_refined_deg 2.366 r_mcangle_it 1.941 r_mcbond_it 1.145 r_chiral_restr 0.202 r_bond_refined_d 0.024 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2285 Nucleic Acid Atoms Solvent Atoms 86 Heterogen Atoms 75
Software Software Software Name Purpose SOLVE phasing REFMAC refinement MOSFLM data reduction SCALA data scaling