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The structure of Escherichia coli ZapD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OEZ PDB entry 2OEZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 15 mg/ml ZapD with 1.2 M ammonium sulfate, 100 mM HEPES, pH 7.5, 10 % PEG 600
Crystal Properties Matthews coefficient Solvent content 3.05 59.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.9 α = 90 b = 108.9 β = 90 c = 106.97 γ = 120
Symmetry Space Group P 64 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 RAYONIX MX-300 2014-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97888 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.4 50 95.2 0.078 13.7 7.9 26464 26464 54.8
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 2.4 2.46 96.1 0.76 2.3
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 2OEZ 2.4 48.525 1.34 26453 2628 95.22 0.2511 0.2468 0.2596 0.2881 0.2947 random 74.3
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] 43.69 43.69 100.27
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.094 f_angle_d 0.665 f_chiral_restr 0.025 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1976 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms 15
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing