2ZQP | pdb_00002zqp

Crystal Structure of SecYE translocon from Thermus thermophilus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ZJSthe SecYE structure produced by MD simulation using 2ZJS structure

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29328.5% PEG 3350, 0.18M Na-citrate, 0.015% octaethylene glycol monododecyl ether, 5% glycerol, 0.0001M Pefabloc, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
4.6473.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.876α = 90
b = 91.876β = 90
c = 240.56γ = 90
Symmetry
Space GroupP 43 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152008-04-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.0000SPring-8BL41XU

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
165093.42743

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTthe SecYE structure produced by MD simulation using 2ZJS structure642.92261612393.80.408840.407040.390.445040.41RANDOM368.097
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]
0.310.31-0.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.285
r_dihedral_angle_3_deg20.689
r_dihedral_angle_4_deg20.115
r_dihedral_angle_1_deg7.515
r_angle_refined_deg1.42
r_symmetry_vdw_refined0.494
r_scangle_it0.425
r_nbtor_refined0.323
r_nbd_refined0.276
r_scbond_it0.255
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3594
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing