4BMZ

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 BIS-TRIS PH 5.5, 25% PEG-3350, 0.2 M MGCL2.6H2O
Crystal Properties
Matthews coefficientSolvent content
2.0239.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.445α = 90
b = 67.746β = 104.96
c = 100.089γ = 90
Symmetry
Space GroupI 1 2 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
11.7955.4898.40.0515.84.2404056
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)
11.791.83990.6224.3

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 4BMX1.7955.5538371203198.260.183430.181610.216RANDOM28.446
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]
0.230.29-0.26-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.915
r_dihedral_angle_4_deg15.67
r_dihedral_angle_3_deg13.509
r_dihedral_angle_1_deg5.799
r_scbond_it2.679
r_mcangle_it2.228
r_angle_refined_deg1.843
r_mcbond_it1.719
r_chiral_restr0.132
r_bond_refined_d0.018
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.915
r_dihedral_angle_4_deg15.67
r_dihedral_angle_3_deg13.509
r_dihedral_angle_1_deg5.799
r_scbond_it2.679
r_mcangle_it2.228
r_angle_refined_deg1.843
r_mcbond_it1.719
r_chiral_restr0.132
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
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 Atoms3465
Nucleic Acid Atoms
Solvent Atoms204
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing