4BMX

Native structure of futalosine hydrolase of Helicobacter pylori strain 26695


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3NM4PDB ENTRY 3NM4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1PROTEIN WAS CRYSTALLIZED IN 4.0 M NA/K PHOSPHATE
Crystal Properties
Matthews coefficientSolvent content
2.6753.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.314α = 90
b = 90.573β = 90
c = 108.381γ = 90
Symmetry
Space GroupP 21 21 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 I02DiamondI02

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
11.7654.19980.1315.810.1574146
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)
11.761.7996.90.932.27.5

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 3NM41.7654.24957357285597.7520.1710.16870.2118RANDOM20.842
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]
0.164-0.005-0.159
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.86
r_dihedral_angle_4_deg17.573
r_dihedral_angle_3_deg12.925
r_dihedral_angle_1_deg6.005
r_scangle_it4.294
r_scbond_it2.89
r_mcangle_it2.015
r_angle_refined_deg1.986
r_mcbond_it1.471
r_nbtor_refined0.316
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.86
r_dihedral_angle_4_deg17.573
r_dihedral_angle_3_deg12.925
r_dihedral_angle_1_deg6.005
r_scangle_it4.294
r_scbond_it2.89
r_mcangle_it2.015
r_angle_refined_deg1.986
r_mcbond_it1.471
r_nbtor_refined0.316
r_nbd_refined0.238
r_chiral_restr0.162
r_xyhbond_nbd_refined0.136
r_bond_refined_d0.02
r_gen_planes_refined0.011
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_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_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 Atoms3471
Nucleic Acid Atoms
Solvent Atoms363
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing