6PJ8

Time-resolved structural snapshot of proteolysis by GlpG inside the membrane


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5F5D 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52980.1 M Na-acetate pH 5.5, 3 M NaCl, and 5 % ethylene glycol
Crystal Properties
Matthews coefficientSolvent content
2.2244.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.57α = 90
b = 97.95β = 90
c = 62.55γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702016-03-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE F10.978CHESSF1

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
12.362.5599.55.759921
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.39

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 REPLACEMENTTHROUGHOUT5F5D2.450.01828744699.440.235120.233620.26276RANDOM39.288
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]
3.840.43-4.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.463
r_dihedral_angle_4_deg21.397
r_dihedral_angle_3_deg15.819
r_long_range_B_refined9.013
r_dihedral_angle_1_deg4.94
r_mcangle_it4.519
r_scbond_it3.062
r_mcbond_it2.717
r_angle_refined_deg1.375
r_chiral_restr0.084
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.463
r_dihedral_angle_4_deg21.397
r_dihedral_angle_3_deg15.819
r_long_range_B_refined9.013
r_dihedral_angle_1_deg4.94
r_mcangle_it4.519
r_scbond_it3.062
r_mcbond_it2.717
r_angle_refined_deg1.375
r_chiral_restr0.084
r_bond_refined_d0.012
r_gen_planes_refined0.005
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 Atoms1475
Nucleic Acid Atoms
Solvent Atoms29
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing