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Crystal structure of factor IXa variant V16I K98T Y177T I213V in complex with PPACK
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WPH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 6 mg/mL protein-inhibitor complex,
0.1M MES pH 6.5,
20% PEG6000
Crystal Properties Matthews coefficient Solvent content 2.18 43.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.34 α = 90 b = 65.8 β = 90 c = 97.32 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS3 2M 2014-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8729 ESRF ID23-2
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 27.25 100 0.1505 12.35 16.3 23122 25.07
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 1.968 100 0.8739 3.14 15.2
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 2wph 1.9 27.25 1.38 23119 1174 99.99 0.1683 0.1659 0.1772 0.213 0.2188 HKL reflections copied from pdb entry 2wph 45.21
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 13.072 f_angle_d 0.901 f_chiral_restr 0.036 f_bond_d 0.005 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2220 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms 64
Software Software Software Name Purpose iMOSFLM data reduction Aimless data scaling MOLREP phasing REFMAC refinement Coot model building PHENIX refinement PDB_EXTRACT data extraction