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Crystal structure of a serine protease inhibitor HPI from Hevea brasiliensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 291 Solution 18 Crystal Screen 1: containing 0.2 M Magnesium acetate, 0.1 M Sodium cacodylate at pH 6.5, and 20% w/v Polyethylene glycol 8,000
Crystal Properties Matthews coefficient Solvent content 2.07 40.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.506 α = 90 b = 47.506 β = 90 c = 95.927 γ = 120
Symmetry Space Group P 61 2 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 PIXEL DECTRIS PILATUS 200K OSMIC VARIMAX OPTICS 2022-05-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.74 47.96 100 0.045 0.047 0.014 1 23.8 8.7 7132 22.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.74 1.76 0.43 0.522 0.279 0.88 0.876
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FREE R-VALUE 1.74 25.25 1.36 7086 674 99.93 0.1988 0.1973 0.1962 0.2128 0.2114 29.64
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 9.4283 f_angle_d 1.2349 f_chiral_restr 0.0809 f_bond_d 0.0136 f_plane_restr 0.0082
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 496 Nucleic Acid Atoms Solvent Atoms 44 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling PHASER phasing