5ZNK

Crystal structure of a bacterial ProRS with ligands


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2J3L 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529732-40% (v/v) Pentaerythritol propoxylate (5/4 PO/OH), 0.1-0.2 M KCl, 50 mM HEPES, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.8556.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 129.575α = 90
b = 77.204β = 99.33
c = 73.965γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2017-12-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U10.979SSRFBL17U1

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
12.075097.40.05311.33.142784
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)
12.072.1397.50.1974

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 REPLACEMENTTHROUGHOUT2J3L2.075040645220297.360.229630.228290.25449RANDOM32.453
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]
0.06-0.16-0.140.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.18
r_dihedral_angle_3_deg13.462
r_dihedral_angle_4_deg12.905
r_dihedral_angle_1_deg6.3
r_long_range_B_refined3.188
r_long_range_B_other3.188
r_mcangle_it1.708
r_mcangle_other1.708
r_scangle_other1.557
r_angle_refined_deg1.259
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.18
r_dihedral_angle_3_deg13.462
r_dihedral_angle_4_deg12.905
r_dihedral_angle_1_deg6.3
r_long_range_B_refined3.188
r_long_range_B_other3.188
r_mcangle_it1.708
r_mcangle_other1.708
r_scangle_other1.557
r_angle_refined_deg1.259
r_mcbond_it0.972
r_mcbond_other0.972
r_angle_other_deg0.906
r_scbond_it0.878
r_scbond_other0.878
r_chiral_restr0.069
r_bond_refined_d0.008
r_bond_other_d0.006
r_gen_planes_refined0.004
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 Atoms4377
Nucleic Acid Atoms
Solvent Atoms127
Heterogen Atoms62

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing