5FXT

Crystal Structure of Helicobacter pylori beta clamp in complex with Carprofen


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4RKIPDB ENTRY 4RKI

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16% W/V PEG 20000, 20% V/V PEG MME550, 0.01M MGCL2, 0.1M MOPS/HEPES-NA PH7.3, 0.2M AMMONIUM CITRATE
Crystal Properties
Matthews coefficientSolvent content
2.6653.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.921α = 90
b = 66.445β = 115.56
c = 82.867γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray287CCDMARRESEARCH2015-11-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM14ESRFBM14

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
11.9750990.0538.84.2308110.3
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)
11.97279.70.223.53.6

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 4RKI1.9774.7629254155799.020.210090.207310.26049RANDOM52.885
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]
3.812.36-4.14-1.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.17
r_dihedral_angle_4_deg17.874
r_dihedral_angle_3_deg16.811
r_dihedral_angle_1_deg7.627
r_mcangle_it3.928
r_scbond_it2.755
r_mcbond_it2.558
r_mcbond_other2.555
r_angle_refined_deg1.956
r_angle_other_deg1.048
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.17
r_dihedral_angle_4_deg17.874
r_dihedral_angle_3_deg16.811
r_dihedral_angle_1_deg7.627
r_mcangle_it3.928
r_scbond_it2.755
r_mcbond_it2.558
r_mcbond_other2.555
r_angle_refined_deg1.956
r_angle_other_deg1.048
r_chiral_restr0.122
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_bond_other_d0.002
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 Atoms2930
Nucleic Acid Atoms
Solvent Atoms74
Heterogen Atoms19

Software

Software
Software NamePurpose
REFMACrefinement
CCP4phasing