X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.5
Temperature 298.0
Details 15% PEG 4000, 0.2 M NaCl, 0.1 M Na-citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 117.29 α = 90
b = 117.29 β = 90
c = 321.87 γ = 120
Symmetry
Space Group P 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2010-10-08
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X25 1.1000 NSLS X25

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
3.1 45.91 82.8 0.067 -- -- 2.0 89814 74374 0.0 0.0 52.48
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)
3.1 3.21 87.5 0.236 -- 3.0 1.9 7834

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
fourier synthesis 3.101 45.906 -- 0.0 89814 74374 4373 82.8 0.2303 0.2303 0.2052 0.2549 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 3.1667 3.2163 -- 667 2612 0.3155 0.4216 -- 69.0
X Ray Diffraction 3.2163 3.2692 -- 0 3413 0.3164 0.0 -- 88.0
X Ray Diffraction 3.2692 3.3258 -- 0 3299 0.3029 0.0 -- 86.0
X Ray Diffraction 3.3258 3.3865 -- 153 3202 0.2876 0.3587 -- 83.0
X Ray Diffraction 3.3865 3.4519 -- 491 2854 0.2639 0.3223 -- 74.0
X Ray Diffraction 3.4519 3.5226 -- 0 3269 0.269 0.0 -- 86.0
X Ray Diffraction 3.5226 3.5995 -- 0 3261 0.2499 0.0 -- 85.0
X Ray Diffraction 3.5995 3.6837 -- 355 2957 0.2501 0.2988 -- 76.0
X Ray Diffraction 3.6837 3.7762 -- 288 2964 0.233 0.2862 -- 77.0
X Ray Diffraction 3.7762 3.8789 -- 0 3220 0.2238 0.0 -- 84.0
X Ray Diffraction 3.8789 3.9937 -- 0 3243 0.2137 0.0 -- 84.0
X Ray Diffraction 3.9937 4.1235 -- 480 2715 0.2059 0.2866 -- 71.0
X Ray Diffraction 4.1235 4.2719 -- 156 3011 0.1911 0.2631 -- 79.0
X Ray Diffraction 4.2719 4.4443 -- 0 3210 0.1739 0.0 -- 83.0
X Ray Diffraction 4.4443 4.6484 -- 0 3131 0.16 0.0 -- 82.0
X Ray Diffraction 4.6484 4.8961 -- 612 2554 0.1768 0.2315 -- 66.0
X Ray Diffraction 4.8961 5.2067 -- 1 3062 0.1782 0.0134 -- 80.0
X Ray Diffraction 5.2067 5.615 -- 0 3054 0.2062 0.0 -- 79.0
X Ray Diffraction 5.615 6.1916 -- 0 3009 0.2344 0.0 -- 78.0
X Ray Diffraction 6.1916 7.1142 -- 571 2362 0.2235 0.2711 -- 62.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.077
f_dihedral_angle_d 17.548
f_angle_d 1.205
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19475
Nucleic Acid Atoms 0
Heterogen Atoms 160
Solvent Atoms 18

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (phenix.refine: 1.8_1069) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8_1069) refinement
PHENIX model building
HKL-2000 data collection