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Crystal structure of Desulfovibrio vulgaris rubrerythrin all-iron(II) form, azide adduct
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RYT Rubrerythrin all-iron(II) form
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.3 298 PEG 1450, MOPS, Sodium Azide, Sodium Dithionite, NADH, BenC, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.25 45.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.344 α = 90 b = 80.092 β = 90 c = 100.168 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 IMAGE PLATE RIGAKU RAXIS IV Confocal Maxflux Optics 2000-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 1.64 50 89.4 0.058 46.5 6.1 21668 21668 18.9
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 1.64 1.7 46.2 0.186 5.1 1.1 1098
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION Difference Fourier analysis THROUGHOUT Rubrerythrin all-iron(II) form 1.64 23.37 21668 21509 1700 88.6 0.18 0.178 0.178 0.202 RANDOM 17.5
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] 6.43 -3.2 -3.23
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 19.4 c_scangle_it 3.06 c_scbond_it 2.04 c_mcangle_it 1.48 c_angle_deg 1.1 c_mcbond_it 1.02 c_improper_angle_d 0.73 c_bond_d 0.005 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 19.4 c_scangle_it 3.06 c_scbond_it 2.04 c_mcangle_it 1.48 c_angle_deg 1.1 c_mcbond_it 1.02 c_improper_angle_d 0.73 c_bond_d 0.005 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 1514 Nucleic Acid Atoms Solvent Atoms 262 Heterogen Atoms 9
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling CNS phasing