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Hemerythrin-like domain of DcrH (met)
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) PEG 4000, 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 2.15 42.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.311 α = 95.27 b = 44.873 β = 104.2 c = 48.127 γ = 90.03
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 0.84 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 1.4 20 96.5 0.064 18.842 3.8 51015 -3 10.842
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) 1.4 1.45 89.7 0.3 2.7 3.3 4748
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 1.4 20 51013 2549 96.34 0.2027 0.2114 0.2294 0.2106 RANDOM 8.233
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] -0.508 0.045 0.001 0.154 0.1 0.372
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.376 r_dihedral_angle_4_deg 15.914 r_dihedral_angle_3_deg 12.908 r_dihedral_angle_1_deg 3.887 r_scangle_it 3.715 r_scbond_it 2.383 r_angle_refined_deg 1.475 r_mcangle_it 1.402 r_mcbond_it 0.781 r_chiral_restr 0.096
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.376 r_dihedral_angle_4_deg 15.914 r_dihedral_angle_3_deg 12.908 r_dihedral_angle_1_deg 3.887 r_scangle_it 3.715 r_scbond_it 2.383 r_angle_refined_deg 1.475 r_mcangle_it 1.402 r_mcbond_it 0.781 r_chiral_restr 0.096 r_bond_refined_d 0.014 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2246 Nucleic Acid Atoms Solvent Atoms 274 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 HKL-2000 data scaling