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X-ray crystal structure of Desulfovibrio vulgaris Rubrerythrin with displacement of iron by zinc at the diiron Site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LKM PDB ENTRY 1LKM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.3 298 PEG 1450, Tris, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.27 45.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.701 α = 90 b = 80.29 β = 90 c = 100.066 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 100 CCD ADSC QUANTUM 210 2001-12-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0 APS 17-ID
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 1.75 11.95 99.7 0.041 20.1 38307 38307 17.1
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 1.75 1.81 99.6 0.117 11.3 2010
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 1LKM 1.75 11.95 38150 37486 2940 98.3 0.178 0.178 0.1882 0.196 0.2057 RANDOM 19.6
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] 5.65 -2.92 -2.72
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 19.3 c_scangle_it 3.11 c_scbond_it 2.04 c_mcangle_it 1.52 c_mcbond_it 1.08 c_angle_deg 1 c_improper_angle_d 0.7 c_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1514 Nucleic Acid Atoms Solvent Atoms 239 Heterogen Atoms 3
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling CNS phasing