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Crystal structure of Trypsin complexed with (3-methoxyphenyl)methanamine (F04 and A06, cocktail experiment)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S0R PDB ENTRY 1S0R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 0.1M Tris-HCl, 30% PEG 3350, 0.2M Lithium Sulfate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.26 45.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.444 α = 90 b = 58.063 β = 90 c = 66.657 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 IMAGE PLATE RIGAKU RAXIS IV++ 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) 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 1.74 50 95.3 0.068 0.068 7.3 21310 -3 19.1
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 (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 1S0R 1.74 19.86 20193 20078 1074 99.43 0.16292 0.16208 0.1764 0.17833 0.1729 RANDOM 12.897
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] -0.15 0.11 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.953 r_dihedral_angle_4_deg 17.787 r_dihedral_angle_3_deg 10.998 r_dihedral_angle_1_deg 6.151 r_scangle_it 1.768 r_scbond_it 1.158 r_angle_refined_deg 1.068 r_angle_other_deg 0.793 r_mcangle_it 0.727 r_mcbond_it 0.453
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.953 r_dihedral_angle_4_deg 17.787 r_dihedral_angle_3_deg 10.998 r_dihedral_angle_1_deg 6.151 r_scangle_it 1.768 r_scbond_it 1.158 r_angle_refined_deg 1.068 r_angle_other_deg 0.793 r_mcangle_it 0.727 r_mcbond_it 0.453 r_symmetry_vdw_other 0.27 r_nbd_refined 0.239 r_symmetry_hbond_refined 0.216 r_nbd_other 0.188 r_nbtor_refined 0.17 r_symmetry_vdw_refined 0.151 r_xyhbond_nbd_refined 0.105 r_mcbond_other 0.084 r_nbtor_other 0.083 r_chiral_restr 0.066 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1629 Nucleic Acid Atoms Solvent Atoms 279 Heterogen Atoms 27
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling