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CRYSTAL STRUCTURE OF THE PEPTIDE(PRO-PRO-GLY)3 BOUND COMPLEX OF N- TERMINAL DOMAIN AND PEPTIDE SUBSTRATE BINDING DOMAIN OF PROLYL-4 HYDROXYLASE (RESIDUES 1-238) TYPE I FROM HUMAN
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YQ8 PDB ENTRY 2YQ8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 10% PEGMME 5000, 10% DMSO, 6% MPD, 0.1 M MES, PH 6.0, 5MM SPERMINE HCL, 5MM (PRO-PRO-GLY)3
Crystal Properties Matthews coefficient Solvent content 2.33 47.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.28 α = 90 b = 100.93 β = 90 c = 68.45 γ = 90
Symmetry Space Group P 21 21 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 MARRESEARCH 2010-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-3 1.0, 1.9 MAX II I911-3
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 1.9 40 99.9 0.09 21.9 19.5 40153 2 34.76
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 1.9 1.95 99.8 0.58 2.4 4.7
Refinement Statistics Diffraction ID Structure Solution 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 2YQ8 1.9 58.765 1.99 40148 1997 99.89 0.1762 0.1738 0.1768 0.2225 0.2211 31.2
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 13.47 f_angle_d 0.931 f_chiral_restr 0.061 f_bond_d 0.007 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3892 Nucleic Acid Atoms Solvent Atoms 281 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing