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Structure of the factor Xa-like trypsin variant triple-Ala (TGPA) in complex with eglin C
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4B2A PDB ENTRIES 4B2A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 283 18% (W/V) PEG 10,000, 20% (V/V) GLYCEROL, 100 MM TRIS-HCL PH 9.0 AND 100 MM NACL AT 283 K
Crystal Properties Matthews coefficient Solvent content 2.03 38.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.34 α = 90 b = 36.94 β = 103.41 c = 103.02 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 CCD MARRESEARCH MIRRORS 2008-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 BESSY 14.1
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 1.36 50 99.6 0.07 13 3.7 123592 -3
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 1.36 1.43 99.9 0.65 2 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 ENTRIES 4B2A 1.36 30 122335 1244 99.61 0.18351 0.1833 0.1835 0.20367 0.2033 RANDOM 15.922
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] 0.33 1.04 -0.54 0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.742 r_dihedral_angle_4_deg 15.581 r_dihedral_angle_3_deg 12.377 r_dihedral_angle_1_deg 6.877 r_angle_refined_deg 2.02 r_chiral_restr 0.137 r_bond_refined_d 0.019 r_gen_planes_refined 0.014 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.742 r_dihedral_angle_4_deg 15.581 r_dihedral_angle_3_deg 12.377 r_dihedral_angle_1_deg 6.877 r_angle_refined_deg 2.02 r_chiral_restr 0.137 r_bond_refined_d 0.019 r_gen_planes_refined 0.014 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4438 Nucleic Acid Atoms Solvent Atoms 540 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing