☰ Navigation Tabs
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 2DYU PDB ENTRY 2DYU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 0.2M lithium sulfate, 0.1M sodium acetate, 14% PEG 2000 MME, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.45 49.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.717 α = 90 b = 130.527 β = 99.44 c = 144.589 γ = 90
Symmetry Space Group C 1 2 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 2005-05-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL12B2 0.9537 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 2.4 30 99.84 3.3 84077 70795
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 2.4 2.49 99.8
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 2DYU 2.5 30 70795 3788 99.84 0.2576 0.25564 0.2557 0.29378 0.2644 RANDOM 9.46
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] 0.03 -0.1 -0.58 0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.147 r_dihedral_angle_4_deg 15.207 r_dihedral_angle_3_deg 13.852 r_dihedral_angle_1_deg 5.384 r_angle_refined_deg 0.882 r_scangle_it 0.583 r_mcangle_it 0.414 r_scbond_it 0.346 r_nbtor_refined 0.321 r_mcbond_it 0.229
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.147 r_dihedral_angle_4_deg 15.207 r_dihedral_angle_3_deg 13.852 r_dihedral_angle_1_deg 5.384 r_angle_refined_deg 0.882 r_scangle_it 0.583 r_mcangle_it 0.414 r_scbond_it 0.346 r_nbtor_refined 0.321 r_mcbond_it 0.229 r_xyhbond_nbd_refined 0.225 r_nbd_refined 0.206 r_symmetry_hbond_refined 0.173 r_symmetry_vdw_refined 0.159 r_chiral_restr 0.064 r_bond_refined_d 0.004 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 14894 Nucleic Acid Atoms Solvent Atoms 850 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing