3PSZ

Crystal Structure of AhQnr, the Qnr protein from Aeromonas hydrophila (P21212 crystal form)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3PSSPDB ENTRY 3PSS

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.82910.1M sodium cacodylate, 1.5M sodium acetate, 20mM DTT, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.957.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.73α = 90
b = 116.29β = 90
c = 55.1γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2008-07-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX10.11.117SRSPX10.1

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
12.243.4398.10.13284.4295762877722.162
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)
2.22.3298.60.4243.14.34050

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 3PSS2.241.4527321145597.330.213790.210850.2699RANDOM16.51
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]
2.16-2.510.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.941
r_dihedral_angle_3_deg13.931
r_dihedral_angle_4_deg13.721
r_dihedral_angle_1_deg6.324
r_scangle_it2.5
r_scbond_it1.588
r_angle_refined_deg1.364
r_mcangle_it0.852
r_angle_other_deg0.845
r_mcbond_it0.466
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.941
r_dihedral_angle_3_deg13.931
r_dihedral_angle_4_deg13.721
r_dihedral_angle_1_deg6.324
r_scangle_it2.5
r_scbond_it1.588
r_angle_refined_deg1.364
r_mcangle_it0.852
r_angle_other_deg0.845
r_mcbond_it0.466
r_mcbond_other0.123
r_chiral_restr0.089
r_bond_refined_d0.012
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3394
Nucleic Acid Atoms
Solvent Atoms249
Heterogen Atoms91

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling