4BMY

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 6.5, 25% PEG-3350, 0.2 M LI2SO4.H2O
Crystal Properties
Matthews coefficientSolvent content
2.2645.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.849α = 90
b = 123.414β = 90
c = 145.853γ = 90
Symmetry
Space GroupC 2 2 21

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
11.6556.8399.90.0816.98.2598126
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)
11.651.6899.60.862.17.9

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 4BMX1.6556.8956753301899.760.170680.169110.20056RANDOM19.998
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]
0.62-0.760.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.805
r_dihedral_angle_4_deg20.067
r_dihedral_angle_3_deg12.017
r_dihedral_angle_1_deg5.803
r_scbond_it1.986
r_angle_refined_deg1.95
r_mcangle_it1.807
r_mcbond_it1.172
r_mcbond_other1.171
r_angle_other_deg0.899
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.805
r_dihedral_angle_4_deg20.067
r_dihedral_angle_3_deg12.017
r_dihedral_angle_1_deg5.803
r_scbond_it1.986
r_angle_refined_deg1.95
r_mcangle_it1.807
r_mcbond_it1.172
r_mcbond_other1.171
r_angle_other_deg0.899
r_chiral_restr0.118
r_bond_refined_d0.019
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
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_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 Atoms3350
Nucleic Acid Atoms
Solvent Atoms417
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing