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Structure of human plasma factor XIIa in complex with (2S)-1-(N,3-dicyclohexyl-D-alanyl)-4-[(4R,5S)-4-methyl-5-phenyl-4,5-dihydro-1,3-oxazol-2-yl]-N-[(thiophen-2-yl)methyl]piperazine-2-carboxamide (compound 8h)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WUB PDb entry 2WUB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.3 291 18% PEG3350, 200 mM lithium sulfate, 0.7 mM cadmium chloride, 100 mM Bis-Tris, pH 6.3
Crystal Properties Matthews coefficient Solvent content 2.64 53.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.121 α = 90 b = 133.413 β = 104.4 c = 88.858 γ = 90
Symmetry Space Group C 1 2 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 6M 2015-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.388 47.258 92.4 0.094 0.995 6.6 3.2 112839
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.388 1.52 0.568
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT PDb entry 2WUB 1.388 47.26 110904 2229 63.5 0.2893 0.2889 0.2898 0.3112 0.3163 RANDOM 10.82
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] -2.1895 0.2019 -1.9698 4.1593
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.18 t_omega_torsion 3.7 t_angle_deg 1.05 t_bond_d 0.008 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5379 Nucleic Acid Atoms Solvent Atoms 303 Heterogen Atoms 137
Software Software Software Name Purpose BUSTER refinement PDB_EXTRACT data extraction XDS data reduction STARANISO data scaling autoBUSTER phasing