1M2V

Crystal Structure of the yeast Sec23/24 heterodimer


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1M2OSec23 from PDB ENTRY 1M2O

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52731.0 M ammonium formate, 18 mM dithiothreitol, 10 % (w/v) xylitol, 0.1 M Hepes pH 7.5, VAPOR DIFFUSION, HANGING DROP at 273K
Crystal Properties
Matthews coefficientSolvent content
2.7254.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.309α = 90
b = 126.371β = 90
c = 180.2γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42002-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X251.050NSLSX25

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
12.752591.20.0625423649463-337.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.752.92

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTSec23 from PDB ENTRY 1M2O2.7519.965423649495238891.20.210.210.257RANDOM52.2
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]
5.877.31-13.19
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.7
c_scangle_it3.03
c_mcangle_it2.47
c_scbond_it1.89
c_angle_deg1.4
c_mcbond_it1.4
c_improper_angle_d0.95
c_bond_d0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11506
Nucleic Acid Atoms
Solvent Atoms69
Heterogen Atoms2

Software

Software
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
CCP4data scaling