4BN0

Structure of futalosine hydrolase mutant of Helicobacter pylori strain 26695


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4BMXPDB ENTRY 4BMX

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.1 M HEPES PH 7.5, 25% PEG-3350, 0.2 M NACL
Crystal Properties
Matthews coefficientSolvent content
1.9938.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.23α = 90
b = 75.69β = 106.38
c = 97.01γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-1DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.1139.6495.10.134.93.5487886
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.112.17980.462.13.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 4BMX2.1139.674248768242594.6620.2120.20920.2614RANDOM27.795
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]
0.6680.1620.545-1.075
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.616
r_dihedral_angle_4_deg20.808
r_dihedral_angle_3_deg16.882
r_dihedral_angle_1_deg6.408
r_angle_refined_deg1.718
r_mcangle_it1.258
r_scangle_it1.217
r_angle_other_deg0.901
r_scbond_it0.726
r_mcbond_it0.723
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.616
r_dihedral_angle_4_deg20.808
r_dihedral_angle_3_deg16.882
r_dihedral_angle_1_deg6.408
r_angle_refined_deg1.718
r_mcangle_it1.258
r_scangle_it1.217
r_angle_other_deg0.901
r_scbond_it0.726
r_mcbond_it0.723
r_mcbond_other0.723
r_nbd_refined0.222
r_nbtor_refined0.179
r_nbd_other0.162
r_xyhbond_nbd_refined0.142
r_chiral_restr0.099
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbtor_other
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6689
Nucleic Acid Atoms
Solvent Atoms165
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing