☰ Navigation Tabs
Structure of thrombin mutant Y225P in the E form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SHH PDB entry 1SHH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.3 295 0.2 M K Formate, 20 % PEG 3350, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.01 38.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.937 α = 90 b = 86.813 β = 90 c = 100.968 γ = 90
Symmetry Space Group P 21 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 100 IMAGE PLATE RIGAKU RAXIS IV++ 2011-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 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 1.9 40 99.3 0.054 27.6 6.6 43725 43419 -0.5 -0.5
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 1.9 1.93 98.2 0.305 4 4.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 PDB entry 1SHH 1.9 35.67 -0.5 41512 41076 2179 99 0.177 0.175 0.1764 0.217 0.2092 RANDOM 36.17
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] 0.02 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.277 r_dihedral_angle_3_deg 16.282 r_dihedral_angle_4_deg 14.967 r_dihedral_angle_1_deg 5.932 r_scangle_it 2.793 r_scbond_it 1.744 r_angle_refined_deg 1.287 r_mcangle_it 1.169 r_mcbond_it 0.638 r_chiral_restr 0.088
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.277 r_dihedral_angle_3_deg 16.282 r_dihedral_angle_4_deg 14.967 r_dihedral_angle_1_deg 5.932 r_scangle_it 2.793 r_scbond_it 1.744 r_angle_refined_deg 1.287 r_mcangle_it 1.169 r_mcbond_it 0.638 r_chiral_restr 0.088 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 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 4582 Nucleic Acid Atoms Solvent Atoms 384 Heterogen Atoms 18
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling