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Helicobacter pylori formamidase AmiF contains a fine-tuned cysteine-glutamate-lysine catalytic triad
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2E2K PDB ENTRY 2E2K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 0.2M lithium sulfate, 0.1M sodium acetate, 6 % PEG 1500, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.27 45.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.089 α = 90 b = 151.795 β = 114.99 c = 89.083 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 113 CCD ADSC QUANTUM 4 2006-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL12B2 1.0 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 2.29 30 91.4 3.4 89656 77740
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 2.29 2.38 92.5
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 2E2K 2.29 30 77697 4162 90.94 0.25501 0.25339 0.2523 0.28469 0.2593 RANDOM 36.601
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] 3.25 -0.17 -0.83 -2.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.546 r_dihedral_angle_4_deg 15.458 r_dihedral_angle_3_deg 13.848 r_dihedral_angle_1_deg 5.069 r_angle_refined_deg 0.947 r_scangle_it 0.621 r_mcangle_it 0.431 r_scbond_it 0.374 r_nbtor_refined 0.302 r_mcbond_it 0.241
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.546 r_dihedral_angle_4_deg 15.458 r_dihedral_angle_3_deg 13.848 r_dihedral_angle_1_deg 5.069 r_angle_refined_deg 0.947 r_scangle_it 0.621 r_mcangle_it 0.431 r_scbond_it 0.374 r_nbtor_refined 0.302 r_mcbond_it 0.241 r_nbd_refined 0.17 r_symmetry_vdw_refined 0.142 r_xyhbond_nbd_refined 0.114 r_symmetry_hbond_refined 0.091 r_chiral_restr 0.061 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 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 15007 Nucleic Acid Atoms Solvent Atoms 735 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing