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Crystal structure of YrbA from Sinorhizobium meliloti in complex with copper.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NFK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 277 0.7 M lithium sulfate
0.02 M copper acetate
0.1 M Tris-HCl, pH 8.5
Crystal Properties Matthews coefficient Solvent content 1.94 36.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.752 α = 90 b = 32.159 β = 90 c = 62.575 γ = 90
Symmetry Space Group P 21 21 21
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 315r 2014-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.722307 ESRF BM30A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 0.8 32.16 99.9 0.084 0.091 0.034 0.999 15 7 465091 66196
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.8 0.81 99 0.856 0.927 0.352 0.727 2.4 6.8 3201
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5NFK 0.8 22.425 1.35 66112 3301 99.9 0.1222 0.1217 0.1218 0.132 0.1311
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.425 f_angle_d 0.898 f_chiral_restr 0.083 f_bond_d 0.032 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 556 Nucleic Acid Atoms Solvent Atoms 150 Heterogen Atoms 2
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling MOLREP phasing