☰ Navigation Tabs
2.9 Angstrom crystal structure of bovine thrombin in tetragonal spacegroup
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 295 3 microliters Bovine thrombin, 7 mg/ml in 0.01M Tris-HCl, ph 8.0, 0.05M NaCl, 0.1M sodium citrate, 20% w/v PEG3350, 15% v/v 2-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.81 56.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.644 α = 90 b = 87.644 β = 90 c = 194.514 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 104 IMAGE PLATE RIGAKU RAXIS IV++ Rigaku Varimax Confocal Optics 2008-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 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 2.8 39.2 85.9 0.167 6.9 4.19 19432 16696
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 2.8 2.9 97.7 0.335 4.3 4.62 1887
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 2.9 15 17545 14714 746 84.6 0.24499 0.24201 0.2479 0.30068 0.2986 RANDOM 35.286
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] -1.07 -1.07 2.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.331 r_dihedral_angle_4_deg 19.952 r_dihedral_angle_3_deg 19.733 r_dihedral_angle_1_deg 4.831 r_angle_refined_deg 1.23 r_scangle_it 0.891 r_scbond_it 0.504 r_mcangle_it 0.459 r_mcbond_it 0.246 r_chiral_restr 0.077
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.331 r_dihedral_angle_4_deg 19.952 r_dihedral_angle_3_deg 19.733 r_dihedral_angle_1_deg 4.831 r_angle_refined_deg 1.23 r_scangle_it 0.891 r_scbond_it 0.504 r_mcangle_it 0.459 r_mcbond_it 0.246 r_chiral_restr 0.077 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4255 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 2
Software Software Software Name Purpose CrystalClear data collection PHENIX model building REFMAC refinement d*TREK data reduction d*TREK data scaling PHENIX phasing