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Crystal structure of a Pseudomonas putida prolyl-4-hydroxylase (P4H) in complex with elongation factor Tu (EF-Tu)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DG1 1DG1, 4J25 experimental model PDB 4J25 1DG1, 4J25
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.8mM MnCl2, 0.9mM OGA, 1mM GDP, 0.1M MgCl2, 22% polyacrylate 5100, 0.1M Hepes pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.98 58.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 200.704 α = 90 b = 200.704 β = 90 c = 74.833 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 ADSC QUANTUM 315r 2012-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.979500 Diamond I04
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 2.697 29.558 99.8 0.086 13.37 47788 -3 74.727
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.86 99.2 0.013 1.437 1.7
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 1DG1, 4J25 2.697 29.558 1.34 47794 47788 2419 99.95 0.1705 0.1679 0.1749 0.2181 0.2201 Random 60.1937
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 15.088 f_angle_d 1.215 f_chiral_restr 0.061 f_bond_d 0.011 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8724 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms 80
Software Software Software Name Purpose XSCALE data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction GDA data collection