X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
Temperature 293.0
Details The purified protein which contained 100 uM m7-GTP was concentrated to about 7 mg/mL in 20 mM Hepes, pH 7.6, 100 mM KCl, 1mM DTT, and 0.1 mM EDTA for crystallization. The m7-GTP-bound eIF4e protein was crystallized with 1:1 ratio of protein solution to reservoir solution of 17-20% PEG-3350 and 0.1-0.4M Na formate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 38.22 α = 90
b = 61.07 β = 90
c = 122.44 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 90
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2007-02-21
Diffraction Radiation
Monochromator Protocol
Single crystal, cylindrically bent, Si(220) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 5.0.1 1.0 ALS 5.0.1

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
2.6 61.2 93.0 0.118 -- -- 2.8 24017 8533 -- 2.2 43.6
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
2.6 2.74 89.3 0.439 -- 1.7 -- 972

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 2.6 36.491 -- -- -- 8121 404 91.27 -- 0.19446 0.19082 0.26715 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 2.6 2.667 560 38 560 0.239 0.369 -- 87.68
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 22.652
Anisotropic B[1][1] -0.58
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.34
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.92
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 0.112
r_dihedral_angle_4_deg 15.987
r_scangle_it 3.803
r_mcangle_it 1.663
r_gen_planes_refined 0.006
r_scbond_it 2.31
r_dihedral_angle_1_deg 6.313
r_bond_refined_d 0.017
r_dihedral_angle_2_deg 38.575
r_dihedral_angle_3_deg 16.929
r_mcbond_it 0.854
r_angle_refined_deg 1.686
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1547
Nucleic Acid Atoms 0
Heterogen Atoms 56
Solvent Atoms 39

Software

Software
Software Name Purpose
BOS data collection
MOLREP phasing
REFMAC refinement version: 5.5.0109
MOSFLM data reduction
SCALA data scaling