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Hemerythrin-like domain of DcrH (semimet-R)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AWY PDB ENTRY 2AWY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 24% (W/V) PEG4000, 0.2M CaCl2, 12% (V/V) isopropanol, 0.1M TrisHCl, pH 8.5, vapor diffusion, hanging drop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.16 42.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.425 α = 95.21 b = 44.903 β = 103.98 c = 48.076 γ = 89.95
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 RIGAKU JUPITER 210 mirrors 2009-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 0.90 SPring-8 BL26B1
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 1.8 20 97.4 0.072 16.259 3.7 24033 -3 17.067
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) 1.8 1.86 95.6 0.358 3.2 3.5 2362
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) 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 PDB ENTRY 2AWY 1.805 20 24026 1195 96.899 0.2471 0.2569 0.2921 0.2587 RANDOM 12.104
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] -0.747 -0.128 0.131 -0.826 -0.135 1.612
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.741 r_dihedral_angle_4_deg 17.918 r_dihedral_angle_3_deg 14.919 r_dihedral_angle_1_deg 4.226 r_scangle_it 2.774 r_scbond_it 1.742 r_angle_refined_deg 1.228 r_mcangle_it 1.079 r_mcbond_it 0.658 r_chiral_restr 0.088
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.741 r_dihedral_angle_4_deg 17.918 r_dihedral_angle_3_deg 14.919 r_dihedral_angle_1_deg 4.226 r_scangle_it 2.774 r_scbond_it 1.742 r_angle_refined_deg 1.228 r_mcangle_it 1.079 r_mcbond_it 0.658 r_chiral_restr 0.088 r_bond_refined_d 0.01 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2246 Nucleic Acid Atoms Solvent Atoms 258 Heterogen Atoms 8
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction SPACE data collection HKL-2000 data reduction