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Crystal structure of the extracellular region of the transmembrane serine protease hepsin with covalently bound preferred substrate.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EKB PDB ENTRY 1EKB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 293 PEG 3350, ammonium fluoride, Na-cacodylate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.16 42.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.705 α = 90 b = 47.633 β = 108.24 c = 67.791 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 90 IMAGE PLATE RIGAKU RAXIS IV OSMIC CONFOCAL OPTIC (GREEN) 2004-02-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.5418
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 1.55 23.9 95 0.056 21.6 6 46843 46843 -3 -3 17
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 1.55 1.61 59.2 0.327 2.1
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 1EKB 1.55 23.9 46821 46821 2367 0.198 0.198 0.196 0.1859 0.217 0.2083 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 c_angle_deg 1.28876 c_bond_d 0.004315
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2829 Nucleic Acid Atoms Solvent Atoms 461 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction TRUNCATE data reduction CNS refinement CCP4 data scaling CNS phasing