4D3G

Structure of PstA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3M05PDB ENTRY 3M05

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.6200 MM NA MALONATE PH=4.6 AND 20% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.2244.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.753α = 90
b = 56.753β = 90
c = 66.165γ = 120
Symmetry
Space GroupP 3 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-10-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 1SOLEILPROXIMA 1

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
1349.121000.1127.238.226727.9
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)
133.161000.567.938.7

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 3M05349.18253613499.780.248490.245750.29267RANDOM82.885
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]
-2.47-1.23-2.478.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.527
r_dihedral_angle_4_deg20.604
r_dihedral_angle_3_deg17.49
r_dihedral_angle_1_deg4.863
r_mcangle_it4.363
r_scbond_it3.602
r_mcbond_it2.682
r_mcbond_other2.674
r_angle_refined_deg1.073
r_angle_other_deg0.707
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.527
r_dihedral_angle_4_deg20.604
r_dihedral_angle_3_deg17.49
r_dihedral_angle_1_deg4.863
r_mcangle_it4.363
r_scbond_it3.602
r_mcbond_it2.682
r_mcbond_other2.674
r_angle_refined_deg1.073
r_angle_other_deg0.707
r_chiral_restr0.054
r_bond_refined_d0.01
r_gen_planes_refined0.003
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
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 Atoms605
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing