3NDB

Crystal structure of a signal sequence bound to the signal recognition particle


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2V3CPDB ENTRY 2V3C

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION5.629130% MPD, 200 mM NH4PO4 (pH 5.6), EVAPORATION, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
3.3262.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.835α = 90
b = 126.275β = 90
c = 201.758γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2009-02-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-11.0ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
1363.898.50.1020.0914.82777839.214.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2V3C3202777826284138598.370.230030.230030.227990.26652RANDOM99.513
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]
-2.787.16-4.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.849
r_dihedral_angle_3_deg25.243
r_dihedral_angle_4_deg19.98
r_dihedral_angle_1_deg7.416
r_scangle_it2.392
r_angle_refined_deg2.068
r_scbond_it1.467
r_mcangle_it1.325
r_mcbond_it0.682
r_chiral_restr0.104
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.849
r_dihedral_angle_3_deg25.243
r_dihedral_angle_4_deg19.98
r_dihedral_angle_1_deg7.416
r_scangle_it2.392
r_angle_refined_deg2.068
r_scbond_it1.467
r_mcangle_it1.325
r_mcbond_it0.682
r_chiral_restr0.104
r_bond_refined_d0.014
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4000
Nucleic Acid Atoms2921
Solvent Atoms
Heterogen Atoms5

Software

Software
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
SCALAdata scaling