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Ascaris suum carboxypeptidase inhibitor in complex with human carboxypeptidase A1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V77 PDB ENTRY 2V77
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 Reservoir solutions were prepared by a Tecan robot and 200-nL crystallization drops were dispensed on 96x3-well CrystalQuick plates (Greiner) by a Cartesian nanodrop robot (Genomic Solutions) at the joint IBMB-CSIC/IRB/Barcelona Science Park High-Throughput Crystallography Platform (PAC). Best crystals appeared after 2-3 weeks in a Bruker steady-temperature crystal farm at 20 C with 0.2 M zinc acetate dihydrate, 0.1 M sodium cacodylate, 9% PEG 8000, pH 6.5 as reservoir solution. These conditions were successfully scaled up to the microliter range with Cryschem crystallization dishes (Hampton Research) using drops containing 3 microl of protein solution (16.5 mg/ml) and 1 microl of reservoir solution, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.2 44.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.47 α = 90 b = 78.7 β = 90 c = 84.5 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 CCD ADSC QUANTUM 315 2008-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.0000 ESRF ID23-1
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 1.6 46.4 99.6 0.086 18.8 7.2 49284 11.6
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 1.6 1.69 97.7 0.499 4.6 7.1 6967
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 (All) 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 2V77 1.6 46.37 49798 48532 752 99.55 0.15769 0.15769 0.15706 0.1557 0.20025 0.1996 RANDOM 12.229
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] 0.56 0.42 -0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.755 r_dihedral_angle_4_deg 14.37 r_dihedral_angle_3_deg 11.949 r_dihedral_angle_1_deg 6.105 r_sphericity_free 4.685 r_scangle_it 3.004 r_sphericity_bonded 2.362 r_scbond_it 2.177 r_mcangle_it 1.323 r_angle_refined_deg 1.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.755 r_dihedral_angle_4_deg 14.37 r_dihedral_angle_3_deg 11.949 r_dihedral_angle_1_deg 6.105 r_sphericity_free 4.685 r_scangle_it 3.004 r_sphericity_bonded 2.362 r_scbond_it 2.177 r_mcangle_it 1.323 r_angle_refined_deg 1.297 r_rigid_bond_restr 1.257 r_mcbond_it 0.894 r_chiral_restr 0.091 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2954 Nucleic Acid Atoms Solvent Atoms 564 Heterogen Atoms 55
Software Software Software Name Purpose ProDC data collection AMoRE phasing REFMAC refinement XDS data reduction SCALA data scaling