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Crystal structure of Escherichia coli protein YodA in complex with Ni - artifact of purification.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OEJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 0.3 ul of 9.6 mg/ml protein in 50mM Tris pH 7.9, 300 mM NaCl and 0.5mM TCEP were mixed with 0.3 ul of the SaltRx condition #65 (2.5 M Ammonium sulfate, 0.1 M BIS-TRIS propane pH 7.0) and equilibrated against 1.5 M NaCl in MRC 2 drops 96 Well Crystallization Plate (Swissci)
Crystal Properties Matthews coefficient Solvent content 2.34 47.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.583 α = 90 b = 76.583 β = 90 c = 61.944 γ = 120
Symmetry Space Group P 31 2 1
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 MARMOSAIC 300 mm CCD 2013-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.978 APS 21-ID-G
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 1.95 50 99.9 0.08 0.08 9 7.3 15647 15635 -3 28.4
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 1.95 1.98 100 0.767 2.41 7.4 750
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 1OEJ 1.951 50 15616 782 99.94 0.1689 0.1666 0.175 0.2154 0.2138 RANDOM 36.632
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] 0.2 0.1 0.2 -0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.206 r_dihedral_angle_4_deg 15.162 r_dihedral_angle_3_deg 14.378 r_dihedral_angle_1_deg 6.492 r_mcangle_it 2.02 r_angle_refined_deg 1.5 r_mcbond_other 1.417 r_mcbond_it 1.416 r_angle_other_deg 0.772 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.206 r_dihedral_angle_4_deg 15.162 r_dihedral_angle_3_deg 14.378 r_dihedral_angle_1_deg 6.492 r_mcangle_it 2.02 r_angle_refined_deg 1.5 r_mcbond_other 1.417 r_mcbond_it 1.416 r_angle_other_deg 0.772 r_chiral_restr 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.006 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1546 Nucleic Acid Atoms Solvent Atoms 137 Heterogen Atoms 31
Software Software Software Name Purpose HKL-3000 data collection HKL-3000 data reduction HKL-3000 data scaling SHELXDE phasing MLPHARE phasing DM phasing Coot model building PDB_EXTRACT data extraction REFMAC refinement DENZO data reduction SCALEPACK data scaling