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Crystal structure of Xaa-Pro aminopeptidase from Escherichia coli K12
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3Q6D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 293 Crystallization solution: 1.4 M Sodium Citrate, 0.1 M Sodium Cacodylate pH 6.6, 10% glycerol, 1 mM ZnCl2 Protein solution: 20 mM TrisHCl, 200 mM NaCl
Crystal Properties Matthews coefficient Solvent content 4.56 73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 224.202 α = 90 b = 224.202 β = 90 c = 74.636 γ = 120
Symmetry Space Group P 32 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 225 mm CCD mirror 2014-01-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON RRCAT INDUS-2 BEAMLINE PX-BL21 0.97947 RRCAT INDUS-2 PX-BL21
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 2.6 48.9 99.9 0.109 10.8 4.1 66134
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 2.6 2.66 99.9 0.673 2.1 4.1
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 3Q6D 2.6 48.897 1.34 66107 3344 99.83 0.2199 0.2188 0.2179 0.2403 0.24 Random selection
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 13.644 f_angle_d 0.995 f_chiral_restr 0.039 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8293 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms 28
Software Software Software Name Purpose PHENIX refinement Coot model building PHENIX model building PHASER phasing Aimless data scaling XDS data processing MAR345dtb data collection