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Carboxypeptidase A Inhibited by a Thiirane Mechanism-Based inactivator
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CTB PDB ENTRY 2CTB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 291 20% PEG 3350, 0.2M AMMONIUM CHLORIDE, 0.02M TRIS, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.97 37.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.319 α = 90 b = 57.504 β = 99.14 c = 57.08 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 MAR CCD 165 mm mirrors 2008-12-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8123 EMBL/DESY, HAMBURG X13
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 1.38 57.544 96.6 0.068 0.068 20 6.1 55180 53703 2 2 9.3
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 1.38 1.46 77.8 0.379 0.379 1.8 5.3 6298
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 2CTB 1.391 20.54 1 1 52590 53692 1102 98.87 0.148 0.148 0.1466 0.162 0.1609 RANDOM 9.564
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] 0.11 -0.09 -0.19 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.444 r_dihedral_angle_4_deg 16.739 r_dihedral_angle_3_deg 10.91 r_dihedral_angle_1_deg 5.571 r_scangle_it 2.006 r_scbond_it 1.383 r_angle_refined_deg 1.137 r_mcangle_it 0.837 r_mcbond_it 0.548 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.444 r_dihedral_angle_4_deg 16.739 r_dihedral_angle_3_deg 10.91 r_dihedral_angle_1_deg 5.571 r_scangle_it 2.006 r_scbond_it 1.383 r_angle_refined_deg 1.137 r_mcangle_it 0.837 r_mcbond_it 0.548 r_nbtor_refined 0.312 r_nbd_refined 0.204 r_symmetry_vdw_refined 0.191 r_symmetry_hbond_refined 0.104 r_chiral_restr 0.078 r_xyhbond_nbd_refined 0.078 r_bond_refined_d 0.008 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2403 Nucleic Acid Atoms Solvent Atoms 323 Heterogen Atoms 57
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection MOSFLM data reduction