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Thrombin-bound boophilin displays a functional and accessible reactive-site loop
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MKX PDB entry 1MKX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 279 18% PEG 8000, 0.05M Potassium phosphate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 279K
Crystal Properties Matthews coefficient Solvent content 3.14 60.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.5 α = 90 b = 104.2 β = 90 c = 129.1 γ = 90
Symmetry Space Group P 21 21 21
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 MAR CCD 165 mm 2004-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 0.93100 ESRF ID14-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.35 54.9 98 0.064 0.064 9.5 3.7 51554 51554 39.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.48 97.4 0.29 0.29 2.6 3.7 7400
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1MKX 2.35 47.19 48886 48886 2627 97.53 0.19235 0.19235 0.1903 0.22995 0.2493 RANDOM 30.989
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] -2.3 1.22 1.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.869 r_dihedral_angle_3_deg 15.964 r_dihedral_angle_4_deg 15.758 r_dihedral_angle_1_deg 5.739 r_angle_refined_deg 1.137 r_mcangle_it 1.119 r_scangle_it 1.019 r_scbond_it 0.642 r_mcbond_it 0.619 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.869 r_dihedral_angle_3_deg 15.964 r_dihedral_angle_4_deg 15.758 r_dihedral_angle_1_deg 5.739 r_angle_refined_deg 1.137 r_mcangle_it 1.119 r_scangle_it 1.019 r_scbond_it 0.642 r_mcbond_it 0.619 r_nbtor_refined 0.302 r_nbd_refined 0.186 r_symmetry_hbond_refined 0.173 r_symmetry_vdw_refined 0.166 r_xyhbond_nbd_refined 0.119 r_chiral_restr 0.081 r_metal_ion_refined 0.048 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 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_other r_symmetry_vdw_other 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 6768 Nucleic Acid Atoms Solvent Atoms 453 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing