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Crystal structure of protein yfiH from Shigella flexneri, Pfam DUF152
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RW0 PDB Entry 1RW0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 Zinc Acetate, Sodium Cacodylate, PEG 8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 20K
Crystal Properties Matthews coefficient Solvent content 2.3 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.683 α = 90.25 b = 50.465 β = 96.51 c = 55.265 γ = 90.29
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 BRANDEIS - B4 mirrors 2004-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X12C 0.979 NSLS X12C
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 2.5 50 0.035 13.2 2.2 18477 18477 25.8
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) 2.5 2.59 95 0.067 2.2
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 1RW0 2.5 33 18477 15869 1576 97.9 0.217 0.217 0.2171 0.283 0.2826 RANDOM 21.9
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] 6.74 -1.43 -1.57 -4.59 0.02 -2.16
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.2 c_scangle_it 2.53 c_angle_deg 2 c_mcangle_it 1.83 c_scbond_it 1.8 c_improper_angle_d 1.13 c_mcbond_it 1.13 c_bond_d 0.01 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.2 c_scangle_it 2.53 c_angle_deg 2 c_mcangle_it 1.83 c_scbond_it 1.8 c_improper_angle_d 1.13 c_mcbond_it 1.13 c_bond_d 0.01 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 3710 Nucleic Acid Atoms Solvent Atoms 191 Heterogen Atoms 2
Software Software Software Name Purpose CNS refinement CBASS data collection HKL-2000 data scaling AMoRE phasing