X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.3
Temperature 295.0
Details Protein: 11.2 mg/ml, 0.5 M sodium chloride, 0.01 M Tris-HCl, Screen: Pegs H1 (Qiagen), 0.2 M K/Na tartrate, 20% (w/v) PEG 3350 Crystals were soaked in a mother liquor containing 20 mM arabinose-5-phosphate for 2 hours before being flash frozen for data collection, VAPOR DIFFUSION, SITTING DROP, temperature 295K, pH 8.3

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 55.04 α = 90
b = 86.2 β = 90
c = 140.55 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD Beryllium lenses 2011-11-02
Diffraction Radiation
Monochromator Protocol
Diamond SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-D 0.97850 APS 21-ID-D

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
1.5 30 99.9 0.071 -- -- 5.9 106919 106919 -- -3.0 --
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)
1.5 1.53 99.9 0.556 -- 4.0 5.7 5295

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 1.5 30.0 -- -- 106919 101536 5316 99.5 0.15181 0.15181 0.15056 0.17527 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 1.502 1.541 -- 345 6707 0.202 0.232 -- 94.73
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 18.775
Anisotropic B[1][1] 0.37
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.28
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.65
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.022
r_dihedral_angle_2_deg 36.259
r_angle_refined_deg 2.057
r_dihedral_angle_3_deg 11.269
r_gen_planes_other 0.001
r_bond_other_d 0.001
r_chiral_restr 0.126
r_dihedral_angle_1_deg 4.407
r_angle_other_deg 1.04
r_gen_planes_refined 0.01
r_dihedral_angle_4_deg 14.272
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4847
Nucleic Acid Atoms 0
Heterogen Atoms 79
Solvent Atoms 723

Software

Software
Software Name Purpose
Blu-Ice data collection version: Max
PHASER phasing
REFMAC refinement version: 5.6.0117
HKL-2000 data reduction
HKL-2000 data scaling