4YHQ

Crystal structure of multidrug resistant clinical isolate PR20 with GRL-5010A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3UCB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52981.15M sodium chloride, 0.1M sodium acetate pH 5.5 and 0.01M Yittrium chloride
Crystal Properties
Matthews coefficientSolvent content
2.141.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.303α = 90
b = 60.303β = 90
c = 86.141γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCD2013-10-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID0.8APS22-ID

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
11.35094.60.05228.55.941329
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)
11.31.3573.80.4093.44.5

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 REPLACEMENTTHROUGHOUT3UCB1.3504132920791000.157320.154660.20986RANDOM19.838
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]
0.230.120.23-0.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg46.755
r_dihedral_angle_4_deg21.484
r_dihedral_angle_3_deg19.235
r_dihedral_angle_1_deg8.563
r_scangle_it7.693
r_scbond_it5.622
r_mcangle_it4.17
r_rigid_bond_restr2.931
r_mcbond_it2.875
r_angle_refined_deg2.749
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg46.755
r_dihedral_angle_4_deg21.484
r_dihedral_angle_3_deg19.235
r_dihedral_angle_1_deg8.563
r_scangle_it7.693
r_scbond_it5.622
r_mcangle_it4.17
r_rigid_bond_restr2.931
r_mcbond_it2.875
r_angle_refined_deg2.749
r_chiral_restr0.192
r_bond_refined_d0.028
r_gen_planes_refined0.015
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_other
r_long_range_B_refined
r_long_range_B_other
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1518
Nucleic Acid Atoms
Solvent Atoms175
Heterogen Atoms62

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing