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CRYSTAL STRUCTURE OF RTX DOMAIN BLOCK V OF ADENYLATE CYCLASE TOXIN FROM BORDETELLA PERTUSSIS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CVW PDB ENTRY 5CVW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291.15 BUFFER COMPOSITION: 5 mM TRIS-HCL PH=7.4, 150 mM NaCl, 10 mM CaCl2. PRECIPITANT COMPOSITION: 0.2 M MAGNESIUM NITRATE, 20% V/V PEG 3350,
Crystal Properties Matthews coefficient Solvent content 2.08 40.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.225 α = 90 b = 52.225 β = 90 c = 195.952 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 90 CCD MARMOSAIC 225 mm CCD 2 MIRRORS 2012-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918410 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 1.45 50 99.9 0.056 22.11 8.55 46709 -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 1.45 1.54 99.8 0.787 2.55
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 5CVW 1.45 32.15 46709 2458 99.9 0.151 0.148 0.1481 0.207 0.2066 RANDOM 22.57
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.037 r_sphericity_free 29.623 r_sphericity_bonded 19.239 r_dihedral_angle_4_deg 19.128 r_dihedral_angle_3_deg 14.331 r_rigid_bond_restr 6.18 r_dihedral_angle_1_deg 6.163 r_angle_refined_deg 1.92 r_chiral_restr 0.148 r_bond_refined_d 0.019
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.037 r_sphericity_free 29.623 r_sphericity_bonded 19.239 r_dihedral_angle_4_deg 19.128 r_dihedral_angle_3_deg 14.331 r_rigid_bond_restr 6.18 r_dihedral_angle_1_deg 6.163 r_angle_refined_deg 1.92 r_chiral_restr 0.148 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2172 Nucleic Acid Atoms Solvent Atoms 221 Heterogen Atoms 24
Software Software Software Name Purpose MOSFLM data reduction PHASER phasing REFMAC refinement XDS data scaling