5Z2V

Crystal structure of RecR from Pseudomonas aeruginosa PAO1


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72931.26M sodium phosphate mono basic monohydrate, 0.14M potassium phosphate dibasic, 10% PEG 6000, 100mM HEPES/sodium hydroxide pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.9458

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.075α = 90
b = 70.075β = 90
c = 369.022γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2016-04-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL19U10.97776SSRFBL19U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim I (All)CC (Half)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
12.25099.70.0340.99920.32027394
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.2497.90.2150.9493.315

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 REPLACEMENTTHROUGHOUT3vdp2.25025500189594.50.180.1780.213RANDOM30.52
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]
0.070.040.07-0.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.555
r_dihedral_angle_4_deg16.404
r_dihedral_angle_3_deg13.533
r_long_range_B_other9.184
r_long_range_B_refined9.182
r_scangle_other7.503
r_dihedral_angle_1_deg5.486
r_scbond_it5.384
r_scbond_other5.382
r_mcangle_other3.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.555
r_dihedral_angle_4_deg16.404
r_dihedral_angle_3_deg13.533
r_long_range_B_other9.184
r_long_range_B_refined9.182
r_scangle_other7.503
r_dihedral_angle_1_deg5.486
r_scbond_it5.384
r_scbond_other5.382
r_mcangle_other3.79
r_mcangle_it3.786
r_mcbond_it2.59
r_mcbond_other2.581
r_angle_refined_deg1.584
r_angle_other_deg1.082
r_chiral_restr0.119
r_bond_refined_d0.011
r_gen_planes_refined0.006
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2938
Nucleic Acid Atoms
Solvent Atoms182
Heterogen Atoms33

Software

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