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The crystal structure of viral collagen prolyl hydroxylase vCPH from Paramecium Bursaria Chlorella virus-1 - 2OG complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JIG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 0.1 M [Imidazole; MES monohydrate (acid)], 0.1 M amino acids [0.2 M L-Na-Glutamate; 0.2 M Alanine (racemic); 0.2 M Glycine; 0.2M Lysine HCL (racemic); 0.2 M Serine (racemic)], 30 % PEGMME 550 PEG 20K pH 6.5 [Morpheus HT96 condition H1, Molecular Dimensions]
COmplex generated by soaking crystals in mother liquor supplemented with 250 mM ZnSO4 and 100 mM 2-OG for a period of 16 hours.
Crystal Properties Matthews coefficient Solvent content 2.11 41.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.79 α = 90 b = 156.95 β = 90.02 c = 41.24 γ = 90
Symmetry Space Group P 1 21 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 PILATUS 2M 2012-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.598 28.43 98 13.55 3.4 55206
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 2JIG 1.598 28.427 2.01 55202 1978 97.67 0.1787 0.1775 0.1878 0.2112 0.2216 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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.632 f_angle_d 1.483 f_chiral_restr 0.076 f_bond_d 0.016 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2907 Nucleic Acid Atoms Solvent Atoms 396 Heterogen Atoms 23
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing