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Bacillus stearothermophilus YhfR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TIP PDB ENTRIES 1TIP, 5PGM +HOMOLOGY MODEL experimental model PDB 5PGM PDB ENTRIES 1TIP, 5PGM +HOMOLOGY MODEL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 45 % POLYETHYLENE GLYCOL 4,000, 120 MM LITHIUM SULFATE, 20 MM TRIS.HCL BUFFER, PH 8.0
Crystal Properties Matthews coefficient Solvent content 2.72 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.2 α = 90 b = 55.2 β = 90 c = 164.43 γ = 90
Symmetry Space Group P 41 21 2
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 OXFORD 2001-01-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM APS 19-BM
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 45.83 99.5 0.109 19.5 12.2 11896 33.2
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 2.4 98.8 0.706 1.3 11.3
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 PDB ENTRIES 1TIP, 5PGM +HOMOLOGY MODEL 2.3 45.83 11896 599 99.1 0.23 0.23 0.2397 0.263 0.2301 RANDOM 54
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] 9.05 12.53 -21.58
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.4 c_scangle_it 5.2 c_scbond_it 3.58 c_mcangle_it 3.21 c_mcbond_it 2.07 c_angle_deg 1.3 c_improper_angle_d 0.8 c_bond_d 0.006 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.4 c_scangle_it 5.2 c_scbond_it 3.58 c_mcangle_it 3.21 c_mcbond_it 2.07 c_angle_deg 1.3 c_improper_angle_d 0.8 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 1623 Nucleic Acid Atoms Solvent Atoms 33 Heterogen Atoms 43
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing