5O2K

Native apo-structure of Pseudomonas stutzeri PtxB to 2.1 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52900.1 M tri-sodium citrate pH 5.5 and 20 % (w/v) PEG 3000
Crystal Properties
Matthews coefficientSolvent content
2.7354.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.947α = 90
b = 136.64β = 115.02
c = 90.843γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-02-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97951DiamondI04

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
12.179.7599.90.0780.9926.36.7113030
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)
12.12.1498.70.6250.5351.26.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.179.69107119560599.620.23860.236240.28218RANDOM36.041
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]
-1.560.21-1.772.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.968
r_dihedral_angle_4_deg17.838
r_dihedral_angle_3_deg15.215
r_dihedral_angle_1_deg6.767
r_long_range_B_refined5.348
r_long_range_B_other5.344
r_scangle_other3.774
r_mcangle_other3.412
r_mcangle_it3.411
r_scbond_it2.366
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.968
r_dihedral_angle_4_deg17.838
r_dihedral_angle_3_deg15.215
r_dihedral_angle_1_deg6.767
r_long_range_B_refined5.348
r_long_range_B_other5.344
r_scangle_other3.774
r_mcangle_other3.412
r_mcangle_it3.411
r_scbond_it2.366
r_scbond_other2.366
r_mcbond_it2.207
r_mcbond_other2.204
r_angle_refined_deg1.521
r_angle_other_deg0.967
r_chiral_restr0.084
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms12055
Nucleic Acid Atoms
Solvent Atoms300
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing