X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Details YSCD150-347 G283P CRYSTALS GREW FROM EQUAL VOLUMES OF PROTEIN (5.8 MG/ML IN 20 MM HEPES PH 7.0, 60 MM NACL) WITH PRECIPITANT SOLUTION (0.15 M NAH2PO4, 20 % (W/V) PEG 3350, 60 MM NACL) IN HANGING-DROP VAPOR-DIFFUSION CRYSTALLIZATION TRAYS AT 292 K (EASYXTAL; QIAGEN).

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 37.99 α = 90
b = 51.55 β = 106.08
c = 50.63 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 (MX-225) MARRESEARCH -- 2011-06-16
Diffraction Radiation
Monochromator Protocol
KMC-1 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.1 -- BESSY 14.1

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
1.4 29.8 95.5 0.04 -- -- 3.7 -- 36930 -- 2.0 13.94
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)
1.4 1.48 99.7 0.55 -- 2.3 3.5 --

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
OTHER 1.4 29.791 -- 1.99 -- 36927 1847 99.55 -- 0.1912 0.1894 0.2258 --
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 1.4001 1.4379 -- 142 2689 0.2865 0.359 -- 100.0
X Ray Diffraction 1.4379 1.4802 -- 141 2680 0.2533 0.3084 -- 100.0
X Ray Diffraction 1.4802 1.528 -- 143 2727 0.22 0.2416 -- 100.0
X Ray Diffraction 1.528 1.5826 -- 141 2684 0.1938 0.2331 -- 100.0
X Ray Diffraction 1.5826 1.646 -- 143 2701 0.2012 0.2445 -- 100.0
X Ray Diffraction 1.646 1.7209 -- 141 2688 0.1944 0.2354 -- 100.0
X Ray Diffraction 1.7209 1.8116 -- 142 2702 0.1819 0.2103 -- 100.0
X Ray Diffraction 1.8116 1.9251 -- 140 2652 0.2047 0.2341 -- 98.0
X Ray Diffraction 1.9251 2.0737 -- 140 2669 0.196 0.2211 -- 99.0
X Ray Diffraction 2.0737 2.2823 -- 142 2682 0.1943 0.233 -- 99.0
X Ray Diffraction 2.2823 2.6124 -- 142 2712 0.1837 0.1968 -- 100.0
X Ray Diffraction 2.6124 3.2907 -- 143 2719 0.1775 0.2324 -- 100.0
X Ray Diffraction 3.2907 29.7973 -- 147 2775 0.1712 0.2086 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -0.7547
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.4714
Anisotropic B[2][2] 2.7898
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.0351
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_chiral_restr 0.082
f_dihedral_angle_d 15.041
f_angle_d 1.238
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1562
Nucleic Acid Atoms 0
Heterogen Atoms 11
Solvent Atoms 289

Software

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
AUTO-RICKSHAW Structure Solution
PHENIX (PHENIX.REFINE) Structure Refinement
Software
Software Name Purpose
PHENIX version: (PHENIX.REFINE) refinement
AUTO-RICKSHAW model building