X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 293.0
Details 0.2 M ammonium acetate, 10% PEG 3350, 0.2 M BIS-TRIS pH 6.5, Protein concentration: 8 mg/mL, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 59.36 α = 90
b = 122.89 β = 111.09
c = 63.14 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2011-06-12
Diffraction Radiation
Monochromator Protocol
channel cut cryogenically cooled monochromator crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.98011 SOLEIL PROXIMA 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
2.35 45 97.0 0.182 -- -- 3.72 35379 34318 -- -3.0 29.17
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)
2.35 2.49 94.3 0.709 -- 2.74 3.56 5671

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 2.347 42.524 -- 2.0 35379 34312 1712 97.26 -- 0.1823 0.1808 0.2099 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 2.3471 2.4161 -- 133 2594 0.2495 0.2879 -- 94.0
X Ray Diffraction 2.4161 2.4941 -- 140 2656 0.2271 0.2936 -- 96.0
X Ray Diffraction 2.4941 2.5832 -- 143 2715 0.2152 0.2573 -- 97.0
X Ray Diffraction 2.5832 2.6866 -- 142 2689 0.1961 0.2429 -- 97.0
X Ray Diffraction 2.6866 2.8089 -- 144 2734 0.2008 0.2385 -- 98.0
X Ray Diffraction 2.8089 2.957 -- 143 2723 0.191 0.219 -- 98.0
X Ray Diffraction 2.957 3.1422 -- 144 2733 0.1851 0.2294 -- 98.0
X Ray Diffraction 3.1422 3.3847 -- 143 2714 0.1883 0.2095 -- 98.0
X Ray Diffraction 3.3847 3.7251 -- 145 2756 0.1691 0.2093 -- 98.0
X Ray Diffraction 3.7251 4.2637 -- 144 2751 0.1514 0.1698 -- 98.0
X Ray Diffraction 4.2637 5.3701 -- 145 2754 0.1492 0.1659 -- 98.0
X Ray Diffraction 5.3701 42.5308 -- 146 2781 0.1827 0.1968 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic - 1 B-factor per atom
Mean Isotropic B 36.63
Anisotropic B[1][1] -3.7327
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -5.9908
Anisotropic B[2][2] 4.0418
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.3091
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.002
f_chiral_restr 0.038
f_dihedral_angle_d 13.316
f_angle_d 0.667
f_bond_d 0.002
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5615
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 273

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
XDS Data Reduction (intensity integration)
XDS Data Reduction (data scaling)
Phaser Structure Solution
PHENIX (phenix.refine: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.1_743) refinement
Phaser model building
ADSC version: Quantum data collection