5FVE

Crystal Structure of Helicobacter pylori beta clamp in complex with 3, 4-Difluorobenzamide


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
120% V/V PEG MME550, 6% W/V PEG 20000, 0.01M MGCL2, 0.1M MOPS/HEPES-NA PH 7.3, 0.2M AMMONIUM CITRATE
Crystal Properties
Matthews coefficientSolvent content
2.6653.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.071α = 90
b = 66.383β = 115.43
c = 82.778γ = 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
12.075098.50.0633.176.8265890.3
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)
12.075090.90.4235.8

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 4RKI2.0774.7625206134298.530.214460.21270.24732RANDOM49.506
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]
3.282.23-3.52-1.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.599
r_dihedral_angle_4_deg15.393
r_dihedral_angle_3_deg15.093
r_dihedral_angle_1_deg6.761
r_long_range_B_refined4.19
r_long_range_B_other4.141
r_mcangle_it2.461
r_mcangle_other2.461
r_scangle_other2.34
r_mcbond_it1.427
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.599
r_dihedral_angle_4_deg15.393
r_dihedral_angle_3_deg15.093
r_dihedral_angle_1_deg6.761
r_long_range_B_refined4.19
r_long_range_B_other4.141
r_mcangle_it2.461
r_mcangle_other2.461
r_scangle_other2.34
r_mcbond_it1.427
r_mcbond_other1.427
r_scbond_it1.355
r_scbond_other1.355
r_angle_refined_deg1.276
r_angle_other_deg0.848
r_chiral_restr0.072
r_bond_refined_d0.008
r_gen_planes_refined0.004
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2870
Nucleic Acid Atoms
Solvent Atoms92
Heterogen Atoms11

Software

Software
Software NamePurpose
REFMACrefinement
CCP4phasing