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X-ray structure of the complex between human thrombin and the TBA deletion mutant lacking thymine 3 nucleobase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 60% Tacsimate, 1-3% MPEG 5K or PEG 8000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.25 62.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.736 α = 90 b = 120.725 β = 94.22 c = 67.233 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 PIXEL DECTRIS PILATUS 2M MIRROR 2012-07-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.009 ELETTRA 5.2R
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 2.55 50 94.4 0.132 29590
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 2.55 2.63 95.4 0.397
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 THROUGHOUT 2.56 29.62 27048 1430 90.26 0.17114 0.17114 0.16827 0.1746 0.22675 0.2275 RANDOM 37.877
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 r_dihedral_angle_2_deg 32.734 r_dihedral_angle_3_deg 16.2 r_dihedral_angle_4_deg 15.003 r_long_range_B_refined 7.64 r_long_range_B_other 7.572 r_dihedral_angle_1_deg 6.893 r_scangle_other 5.876 r_scbond_it 3.784 r_scbond_other 3.784 r_mcangle_it 3.761
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.734 r_dihedral_angle_3_deg 16.2 r_dihedral_angle_4_deg 15.003 r_long_range_B_refined 7.64 r_long_range_B_other 7.572 r_dihedral_angle_1_deg 6.893 r_scangle_other 5.876 r_scbond_it 3.784 r_scbond_other 3.784 r_mcangle_it 3.761 r_mcangle_other 3.76 r_mcbond_it 2.495 r_mcbond_other 2.494 r_angle_refined_deg 1.693 r_angle_other_deg 1.304 r_chiral_restr 0.097 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.005 r_gen_planes_other 0.004 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 4708 Nucleic Acid Atoms 612 Solvent Atoms 219 Heterogen Atoms 92
Software Software Software Name Purpose CCP4 refinement PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling