X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 293.0
Details 1.7M Li2SO4, 100mM HEPES, 25% PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 59.57 α = 90
b = 85.82 β = 90
c = 176.65 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 ADSC QUANTUM 315 -- 2012-02-17
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRF BEAMLINE BL17U 0.97915 SSRF BL17U

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
1.8 35.48 -- -- -- -- -- 84247 76885 -- -- 23.64

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 1.803 35.477 -- 0.0 84247 76885 3836 91.18 -- 0.2085 0.2069 0.2384 --
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 1.8031 1.8259 -- 122 2365 0.2552 0.3207 -- 81.0
X Ray Diffraction 1.8259 1.8499 -- 137 2488 0.2519 0.2853 -- 86.0
X Ray Diffraction 1.8499 1.8753 -- 108 2460 0.2651 0.3299 -- 83.0
X Ray Diffraction 1.8753 1.9021 -- 96 1705 0.2947 0.3496 -- 58.0
X Ray Diffraction 1.9021 1.9305 -- 134 2564 0.4375 0.4905 -- 88.0
X Ray Diffraction 1.9305 1.9606 -- 82 1901 0.2675 0.2326 -- 64.0
X Ray Diffraction 1.9606 1.9928 -- 142 2556 0.2376 0.2823 -- 87.0
X Ray Diffraction 1.9928 2.0271 -- 143 2730 0.2289 0.283 -- 93.0
X Ray Diffraction 2.0271 2.064 -- 149 2758 0.2159 0.2746 -- 95.0
X Ray Diffraction 2.064 2.1037 -- 151 2730 0.2257 0.271 -- 93.0
X Ray Diffraction 2.1037 2.1466 -- 145 2796 0.2314 0.2835 -- 94.0
X Ray Diffraction 2.1466 2.1933 -- 125 2796 0.2331 0.2523 -- 94.0
X Ray Diffraction 2.1933 2.2443 -- 113 2395 0.2565 0.3367 -- 82.0
X Ray Diffraction 2.2443 2.3004 -- 149 2518 0.277 0.3178 -- 86.0
X Ray Diffraction 2.3004 2.3626 -- 141 2800 0.2132 0.2809 -- 95.0
X Ray Diffraction 2.3626 2.4321 -- 178 2810 0.22 0.2614 -- 97.0
X Ray Diffraction 2.4321 2.5106 -- 170 2887 0.2196 0.2394 -- 98.0
X Ray Diffraction 2.5106 2.6003 -- 137 2936 0.2111 0.2641 -- 98.0
X Ray Diffraction 2.6003 2.7043 -- 149 2936 0.2185 0.2565 -- 99.0
X Ray Diffraction 2.7043 2.8274 -- 135 2961 0.2148 0.2672 -- 99.0
X Ray Diffraction 2.8274 2.9764 -- 162 2978 0.2109 0.2481 -- 99.0
X Ray Diffraction 2.9764 3.1627 -- 157 2957 0.1986 0.2061 -- 100.0
X Ray Diffraction 3.1627 3.4068 -- 159 2965 0.1942 0.2375 -- 100.0
X Ray Diffraction 3.4068 3.7493 -- 153 2848 0.1749 0.1797 -- 94.0
X Ray Diffraction 3.7493 4.291 -- 169 3009 0.154 0.1868 -- 100.0
X Ray Diffraction 4.291 5.4031 -- 138 3080 0.1552 0.1691 -- 100.0
X Ray Diffraction 5.4031 35.4836 -- 192 3120 0.2127 0.2236 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 31.2088
Anisotropic B[1][1] -2.3168
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 6.3537
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.0369
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 15.233
f_plane_restr 0.004
f_chiral_restr 0.075
f_angle_d 1.114
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5963
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 532

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
HKL-2000 Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7_650) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
Phaser version: 2.1.4 molecular replacement
SCALA data reduction