X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.5
Temperature 281.0
Details 0.1M tri-sodium citrate pH 5.5, 20% PEG 3000, VAPOR DIFFUSION, SITTING DROP, temperature 281K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 46.46 α = 70.39
b = 62.79 β = 86.01
c = 83.8 γ = 79.41
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2010-11-01
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 AUSTRALIAN SYNCHROTRON MX2

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
1.65 -- -- 0.077 -- -- 3.9 -- 100941 -- -- 14.61
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)
1.65 1.74 88.2 0.55 -- -- 3.9 --

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
MIR 1.65 19.677 -- 1.98 -- 100915 5038 95.73 -- 0.1661 0.1647 0.1919 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 1.65 1.709 -- 462 8706 0.2693 0.2948 -- 87.0
X Ray Diffraction 1.709 1.7773 -- 486 9553 0.219 0.267 -- 95.0
X Ray Diffraction 1.7773 1.8582 -- 490 9661 0.1866 0.2324 -- 96.0
X Ray Diffraction 1.8582 1.956 -- 477 9581 0.1591 0.2025 -- 96.0
X Ray Diffraction 1.956 2.0785 -- 520 9627 0.1453 0.1792 -- 96.0
X Ray Diffraction 2.0785 2.2387 -- 514 9683 0.1356 0.1731 -- 97.0
X Ray Diffraction 2.2387 2.4637 -- 515 9740 0.1379 0.1727 -- 97.0
X Ray Diffraction 2.4637 2.8193 -- 530 9695 0.1466 0.1765 -- 97.0
X Ray Diffraction 2.8193 3.5486 -- 555 9780 0.1544 0.18 -- 98.0
X Ray Diffraction 3.5486 19.6782 -- 489 9851 0.1788 0.188 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.8516
Anisotropic B[1][1] 9.4533
Anisotropic B[1][2] -4.5168
Anisotropic B[1][3] 2.8299
Anisotropic B[2][2] -7.5568
Anisotropic B[2][3] -1.2857
Anisotropic B[3][3] -0.691
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.078
f_dihedral_angle_d 13.266
f_angle_d 1.187
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6945
Nucleic Acid Atoms 0
Heterogen Atoms 51
Solvent Atoms 679

Software

Computing
Computing Package Purpose
blueice Data Collection
XDS Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (phenix.refine: 1.7_650) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7_650) refinement
PHENIX model building
blueice data collection