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Crystal Structure of the Effector Domain of PhnF from Mycobacterium smegmatis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2P19 PDB ENTRY 2P19
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291 Micro-seeded into 0.65M ammonium sulfate, 0.1M lithium sulfate, 0.1M tris, pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.48 50.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.558 α = 90 b = 78.172 β = 125.42 c = 120.514 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 IMAGE PLATE MAR scanner 345 mm plate 2008-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54179
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 1.9 25.28 100 0.069 8.5 6.8 68334 68334 26.8
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 1.9 2 100 0.491 1.6 3.6 9909
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-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 2P19 1.9 25.1 68333 64877 3456 99.95 0.1818 0.1853 0.1959 0.1994 RANDOM 30.244
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] 1.23 0.78 -0.56 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.067 r_dihedral_angle_4_deg 16.239 r_dihedral_angle_3_deg 13.951 r_dihedral_angle_1_deg 6.527 r_scangle_it 4.015 r_scbond_it 2.522 r_mcangle_it 1.6 r_angle_refined_deg 1.597 r_mcbond_it 0.913 r_chiral_restr 0.105
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.067 r_dihedral_angle_4_deg 16.239 r_dihedral_angle_3_deg 13.951 r_dihedral_angle_1_deg 6.527 r_scangle_it 4.015 r_scbond_it 2.522 r_mcangle_it 1.6 r_angle_refined_deg 1.597 r_mcbond_it 0.913 r_chiral_restr 0.105 r_bond_refined_d 0.015 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4967 Nucleic Acid Atoms Solvent Atoms 631 Heterogen Atoms 62
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection BALBES phasing