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Crystal Structure of a Periplasmic Heme Binding Protein from Shigella dysenteriae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2R79 model of PhuT, PDB ENTRY 2R79
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 298 0.1M sodium citrate, 0.05M ammonium bromide, 15% polyethylene glycol 4000, 0.001M hemin chloride, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.46 49.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.7 α = 70.25 b = 73.308 β = 79.02 c = 73.316 γ = 90.22
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 MARMOSAIC 325 mm CCD mirrors 2006-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 1.00 SSRL BL9-2
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 2.05 43.86 98 0.057 0.057 27.2 3.9 63384 -3 19.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.09 97 0.67 2.01 3.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 model of PhuT, PDB ENTRY 2R79 2.05 43.86 63591 6415 96.5 0.21 0.21 0.203 0.255 0.2486 RANDOM 39
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] -5.5 -6.06 -4.81 0.95 5.26 4.55
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.1 c_scangle_it 3.38 c_scbond_it 2.31 c_mcangle_it 2.25 c_mcbond_it 1.44 c_angle_deg 1.2 c_improper_angle_d 0.92 c_bond_d 0.006 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.1 c_scangle_it 3.38 c_scbond_it 2.31 c_mcangle_it 2.25 c_mcbond_it 1.44 c_angle_deg 1.2 c_improper_angle_d 0.92 c_bond_d 0.006 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7741 Nucleic Acid Atoms Solvent Atoms 499 Heterogen Atoms 43
Software Software Software Name Purpose CNS refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling SOLVE phasing