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Crystal structure of a Kunitz type trypsin inhibitor from Cicer arietinumL
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R8N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293.15 0.1M sodium acetate pH 5, 1M ammonium sulphate
Crystal Properties Matthews coefficient Solvent content 1.97 37.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.73 α = 90 b = 88.22 β = 108.32 c = 59.34 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 100 CCD RAYONIX MX225HE 2016-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON RRCAT INDUS-2 BEAMLINE PX-BL21 0.97947 RRCAT INDUS-2 PX-BL21
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 2.8 56.33 99.6 0.057 12 3.8 9350
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 1R8N 2.8 56.33 8854 476 99.34 0.19736 0.19615 0.2013 0.22052 0.2233 RANDOM 29.791
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] -0.12 0.24 0.93 -0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.988 r_dihedral_angle_4_deg 15.694 r_dihedral_angle_3_deg 15.673 r_dihedral_angle_1_deg 7.328 r_long_range_B_refined 5.077 r_long_range_B_other 5.076 r_scangle_other 3.799 r_angle_other_deg 3.75 r_mcangle_it 3.71 r_mcangle_other 3.709
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.988 r_dihedral_angle_4_deg 15.694 r_dihedral_angle_3_deg 15.673 r_dihedral_angle_1_deg 7.328 r_long_range_B_refined 5.077 r_long_range_B_other 5.076 r_scangle_other 3.799 r_angle_other_deg 3.75 r_mcangle_it 3.71 r_mcangle_other 3.709 r_mcbond_it 2.426 r_scbond_it 2.426 r_scbond_other 2.426 r_mcbond_other 2.425 r_angle_refined_deg 1.568 r_chiral_restr 0.086 r_bond_refined_d 0.015 r_gen_planes_other 0.007 r_gen_planes_refined 0.006 r_bond_other_d r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2717 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing