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Crystal structure of ZnuA from Citrobacter koseri
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XY4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 Protein at 18 mg/mL and containing one molar equivalent of ZnCl2 was combined with an equal volume of reservoir solution containing 0.1 M sodium citrate pH 6.0, 0.05 M ammonium acetate, 1 mM tellurium polyoxo tungstate, and 26% w/v PEG 4000.
Crystal Properties Matthews coefficient Solvent content 2.81 56.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.246 α = 90 b = 81.667 β = 112.99 c = 126.555 γ = 90
Symmetry Space Group P 1 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 PIXEL DECTRIS PILATUS3 6M 2021-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.977408 ALS 5.0.1
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 3.15 47.47 99.8 0.22 0.257 0.131 0.99 5.9 3.7 39993
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 3.15 3.28 99.8 1.692 1.972 1.002 0.339 3.7
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 2XY4 3.15 47.47 37978 2006 99.69 0.2191 0.2173 0.2093 0.2541 0.2515 RANDOM
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] -0.5 2.98 1.25 -1.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.024 r_dihedral_angle_4_deg 20.959 r_dihedral_angle_3_deg 20.236 r_dihedral_angle_1_deg 7.7 r_angle_refined_deg 1.643 r_angle_other_deg 1.104 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.024 r_dihedral_angle_4_deg 20.959 r_dihedral_angle_3_deg 20.236 r_dihedral_angle_1_deg 7.7 r_angle_refined_deg 1.643 r_angle_other_deg 1.104 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.007 r_gen_planes_other 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12144 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 99
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing