2E2K

Helicobacter pylori formamidase AmiF contains a fine-tuned cysteine-glutamate-lysine catalytic triad


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2DYUPDB ENTRY 2DYU

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP52930.2M lithium sulfate, 0.1M sodium acetate, 14% PEG 2000 MME, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4549.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 117.717α = 90
b = 130.527β = 99.44
c = 144.589γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray113CCDADSC QUANTUM 42005-05-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL12B20.9537SPring-8BL12B2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.43099.843.38407770795
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.4999.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2DYU2.53070795378899.840.25760.255640.29378RANDOM9.46
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]
0.03-0.1-0.580.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.147
r_dihedral_angle_4_deg15.207
r_dihedral_angle_3_deg13.852
r_dihedral_angle_1_deg5.384
r_angle_refined_deg0.882
r_scangle_it0.583
r_mcangle_it0.414
r_scbond_it0.346
r_nbtor_refined0.321
r_mcbond_it0.229
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.147
r_dihedral_angle_4_deg15.207
r_dihedral_angle_3_deg13.852
r_dihedral_angle_1_deg5.384
r_angle_refined_deg0.882
r_scangle_it0.583
r_mcangle_it0.414
r_scbond_it0.346
r_nbtor_refined0.321
r_mcbond_it0.229
r_xyhbond_nbd_refined0.225
r_nbd_refined0.206
r_symmetry_hbond_refined0.173
r_symmetry_vdw_refined0.159
r_chiral_restr0.064
r_bond_refined_d0.004
r_gen_planes_refined0.002
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 AtomsNumber
Protein Atoms14894
Nucleic Acid Atoms
Solvent Atoms850
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing