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Helicobacter pylori formamidase AmiF contains a fine-tuned cysteine-glutamate-lysine catalytic triad
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.1M sodium cacodylate, 0.15M potassium thiocyanate, 20% polyethylene glycol 550 MME, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.02 39.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 147.215 α = 90 b = 147.215 β = 90 c = 72.273 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 113 CCD ADSC QUANTUM 4 2004-07-11 M SINGLE WAVELENGTH 2 1 x-ray 113 CCD ADSC QUANTUM 4 2004-07-11 M 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL12B2 0.9800 SPring-8 BL12B2 2 SYNCHROTRON SPRING-8 BEAMLINE BL12B2 0.9791 SPring-8 BL12B2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1,2 1.75 30 99.7 3.2 58786 58786
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1,2 1.75 1.81 100
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.75 30 55500 2960 98.95 0.1764 0.17433 0.1807 0.21515 0.1766 RANDOM 23.57
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] 0.04 0.02 0.04 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.514 r_dihedral_angle_4_deg 16.181 r_dihedral_angle_3_deg 13.278 r_dihedral_angle_1_deg 5.574 r_scangle_it 2.02 r_scbond_it 1.257 r_mcangle_it 1.068 r_angle_refined_deg 1.037 r_mcbond_it 0.611 r_nbtor_refined 0.321
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.514 r_dihedral_angle_4_deg 16.181 r_dihedral_angle_3_deg 13.278 r_dihedral_angle_1_deg 5.574 r_scangle_it 2.02 r_scbond_it 1.257 r_mcangle_it 1.068 r_angle_refined_deg 1.037 r_mcbond_it 0.611 r_nbtor_refined 0.321 r_nbd_refined 0.205 r_xyhbond_nbd_refined 0.191 r_symmetry_hbond_refined 0.189 r_symmetry_vdw_refined 0.146 r_chiral_restr 0.07 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5098 Nucleic Acid Atoms Solvent Atoms 713 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling SOLVE phasing