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Crystal structure of a ternary complex between PSA, a substrat-acyl intermediate and an activating antibody
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZCH pdb entry 2ZCH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.2 293 crystal grown in 14% MPEG550, 100mM HEPES (pH7.2), then soaked in PEG400, 100mM Tris-HCl (pH7.3), 10mM ZnCl2, 0.28 mg/ml Mu-KGISSQY-AFC, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.98 58.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.765 α = 90 b = 86.765 β = 90 c = 238.18 γ = 90
Symmetry Space Group P 41 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 200 CCD ADSC QUANTUM 4 2006-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
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 3.1 70.19 99.2 0.115 0.127 12.8 5.5 17100
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 3.1 3.27 98.4 0.519 0.583 2.3 4.4 2397
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 entry 2ZCH 3.1 70.19 16217 870 98.73 0.2234 0.22064 0.2215 0.27522 0.2788 RANDOM 62.772
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] 1.11 1.11 -2.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.733 r_dihedral_angle_3_deg 18.849 r_dihedral_angle_4_deg 16.009 r_dihedral_angle_1_deg 8.335 r_scangle_it 2.342 r_angle_refined_deg 1.733 r_scbond_it 1.578 r_mcangle_it 1.149 r_mcbond_it 1.136 r_angle_other_deg 0.974
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.733 r_dihedral_angle_3_deg 18.849 r_dihedral_angle_4_deg 16.009 r_dihedral_angle_1_deg 8.335 r_scangle_it 2.342 r_angle_refined_deg 1.733 r_scbond_it 1.578 r_mcangle_it 1.149 r_mcbond_it 1.136 r_angle_other_deg 0.974 r_chiral_restr 0.241 r_nbd_refined 0.211 r_nbd_other 0.201 r_nbtor_refined 0.183 r_symmetry_vdw_refined 0.178 r_symmetry_hbond_refined 0.173 r_xyhbond_nbd_refined 0.166 r_symmetry_vdw_other 0.161 r_nbtor_other 0.091 r_mcbond_other 0.064 r_bond_refined_d 0.015 r_bond_other_d 0.007 r_gen_planes_refined 0.005 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 5273 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection MOSFLM data reduction PROCESS data scaling XFIT data reduction