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Hemerythrin-like domain of DcrH I119H mutant (met)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AGT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.2 283 30 % (W/V) PEG 4000, 0.2M CaCl2, 12% (V/V) isopropanol, 0.1M TrisHCl, pH 8.2, vapor diffusion, hanging drop, temperature 283K
Crystal Properties Matthews coefficient Solvent content 2.08 40.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.573 α = 92.71 b = 44.082 β = 102.59 c = 46.715 γ = 90.02
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 RAYONIX MX225HE mirrors 2013-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.00 SPring-8 BL41XU
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 1.9 30 97.9 0.098 0.098 14.282 4 20052 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.97 96.4 0.323 0.323 4.167 4
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 3AGT 1.9 20 20052 1013 97.7 0.1959 0.1933 0.1931 0.2476 0.2474 RANDOM 12.5531
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] -0.23 -0.23 0.01 -0.82 0.01 0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.551 r_dihedral_angle_4_deg 17.765 r_dihedral_angle_3_deg 14.563 r_dihedral_angle_1_deg 5.118 r_angle_refined_deg 1.356 r_chiral_restr 0.099 r_bond_refined_d 0.012 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2250 Nucleic Acid Atoms Solvent Atoms 270 Heterogen Atoms 10
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 REFMAC phasing