6PGN

PagF single mutant with GPP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5TTYPDB entry 5TTY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP282lithium sulfate, PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.4449.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.662α = 90
b = 116.662β = 90
c = 43.681γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2016-10-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.978560APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.8573.610024.615.629288
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.856

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 5TTY1.852527736153299.940.190340.188910.21556RANDOM26.881
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]
0.240.120.24-0.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.547
r_dihedral_angle_3_deg13.338
r_dihedral_angle_4_deg8.022
r_dihedral_angle_1_deg5.569
r_long_range_B_refined4.329
r_mcangle_it1.846
r_scbond_it1.351
r_angle_refined_deg1.272
r_mcbond_it1.074
r_chiral_restr0.084
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.547
r_dihedral_angle_3_deg13.338
r_dihedral_angle_4_deg8.022
r_dihedral_angle_1_deg5.569
r_long_range_B_refined4.329
r_mcangle_it1.846
r_scbond_it1.351
r_angle_refined_deg1.272
r_mcbond_it1.074
r_chiral_restr0.084
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2462
Nucleic Acid Atoms
Solvent Atoms200
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
autoPROCdata scaling
SHARPphasing