6EK4

PaxB from Photorhabdus luminescens


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52930.2 M MgCl2; 0.1 M Bis-Tris, 25% PEG 3350; 0.2M NaSCN
Crystal Properties
Matthews coefficientSolvent content
2.9358.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.59α = 90
b = 70.18β = 108.41
c = 136.89γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2015-12-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.0SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim 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
12.83095.30.0690.9979.72.944675
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.994.70.5150.7291.8

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 REPLACEMENTTHROUGHOUTSemet derivative of PaxB2.81542429223495.370.242050.24050.26835RANDOM85.879
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]
-3.670.04-2.374.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.621
r_dihedral_angle_3_deg14.744
r_dihedral_angle_4_deg10.761
r_dihedral_angle_1_deg3.992
r_long_range_B_refined3.601
r_long_range_B_other3.554
r_mcangle_it1.527
r_mcangle_other1.527
r_scangle_other1.162
r_mcbond_it0.834
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.621
r_dihedral_angle_3_deg14.744
r_dihedral_angle_4_deg10.761
r_dihedral_angle_1_deg3.992
r_long_range_B_refined3.601
r_long_range_B_other3.554
r_mcangle_it1.527
r_mcangle_other1.527
r_scangle_other1.162
r_mcbond_it0.834
r_mcbond_other0.834
r_angle_refined_deg0.696
r_angle_other_deg0.646
r_scbond_it0.607
r_scbond_other0.607
r_chiral_restr0.041
r_bond_refined_d0.004
r_gen_planes_refined0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10648
Nucleic Acid Atoms
Solvent Atoms226
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing