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TRYPTASE B2 IN COMPLEX WITH 5-(3-Aminomethyl-phenoxymethyl)-3-[3-(2-chloro-pyridin-3-ylethynyl)-phenyl]-oxazolidin-2-one; compound with trifluoro-acetic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other in-house structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 20% PEG 10000, 0.1 M HEPES
Crystal Properties Matthews coefficient Solvent content 2.67 53.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.34 α = 90 b = 78.34 β = 90 c = 165.95 γ = 120
Symmetry Space Group P 31 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 IMAGE PLATE MAR scanner 345 mm plate 2006-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR591 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 1.94 67.88 98.8 0.096 0.0103 5.4 43956
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 1.94 2.06 93.2 0.249 4.78 5.2
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 in-house structure 1.94 67.88 41738 2218 99.39 0.15726 0.15494 0.1634 0.20026 0.2045 RANDOM 15.628
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] 0.33 0.16 0.33 -0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.519 r_dihedral_angle_3_deg 14.031 r_dihedral_angle_4_deg 12.039 r_dihedral_angle_1_deg 6.233 r_scangle_it 2.42 r_scbond_it 1.675 r_angle_refined_deg 1.442 r_mcangle_it 1.074 r_mcbond_it 0.68 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.519 r_dihedral_angle_3_deg 14.031 r_dihedral_angle_4_deg 12.039 r_dihedral_angle_1_deg 6.233 r_scangle_it 2.42 r_scbond_it 1.675 r_angle_refined_deg 1.442 r_mcangle_it 1.074 r_mcbond_it 0.68 r_nbtor_refined 0.314 r_nbd_refined 0.209 r_symmetry_vdw_refined 0.204 r_xyhbond_nbd_refined 0.157 r_symmetry_hbond_refined 0.134 r_chiral_restr 0.1 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3831 Nucleic Acid Atoms Solvent Atoms 689 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement XDS data reduction XPREP data scaling REFMAC phasing