X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.6
Temperature 298.0
Details 23% PEG2000 MME, 0.2 M MAGNESIUM CHLORIDE, 0.1 M BIS-TRIS, PH 6.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 41.54 α = 90
b = 127.45 β = 90.04
c = 70.77 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 MARMOSAIC 300 mm CCD -- 2011-04-07
Diffraction Radiation
Monochromator Protocol
SI(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-B 1.28162 APS 23-ID-B

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
2.2 19.93 99.8 0.078 -- -- 7.5 -- 36252 -- 1.0 --
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)
2.2 2.32 100.0 0.559 -- 3.6 7.5 --

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
SAD 2.2 19.93 -- 0.19 -- 36218 1953 97.3 -- 0.192 0.189 0.236 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 2.2 2.255 -- 132 2273 0.2525 0.2922 -- 93.0
X Ray Diffraction 2.255 2.3159 -- 133 2374 0.2271 0.2894 -- 93.0
X Ray Diffraction 2.3159 2.3839 -- 134 2366 0.222 0.2843 -- 95.0
X Ray Diffraction 2.3839 2.4607 -- 137 2408 0.2131 0.2726 -- 95.0
X Ray Diffraction 2.4607 2.5485 -- 137 2387 0.2229 0.2803 -- 95.0
X Ray Diffraction 2.5485 2.6503 -- 142 2448 0.2399 0.3512 -- 97.0
X Ray Diffraction 2.6503 2.7706 -- 141 2447 0.2401 0.3101 -- 98.0
X Ray Diffraction 2.7706 2.9163 -- 141 2497 0.216 0.2844 -- 98.0
X Ray Diffraction 2.9163 3.0984 -- 140 2460 0.2176 0.249 -- 99.0
X Ray Diffraction 3.0984 3.3366 -- 140 2487 0.1924 0.2506 -- 99.0
X Ray Diffraction 3.3366 3.6704 -- 139 2500 0.1674 0.2185 -- 99.0
X Ray Diffraction 3.6704 4.1972 -- 146 2546 0.1653 0.2054 -- 100.0
X Ray Diffraction 4.1972 5.2718 -- 147 2518 0.1423 0.1674 -- 100.0
X Ray Diffraction 5.2718 19.9317 -- 144 2554 0.1783 0.2053 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -7.2617
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.4644
Anisotropic B[2][2] -9.5208
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 16.7825
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.002
f_chiral_restr 0.043
f_dihedral_angle_d 17.146
f_angle_d 0.682
f_bond_d 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4053
Nucleic Acid Atoms 1036
Heterogen Atoms 6
Solvent Atoms 253

Software

Computing
Computing Package Purpose
XDS Data Collection
XDS Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (PHENIX.REFINE: 1.6.4_486) Structure Refinement
Software
Software Name Purpose
PHENIX version: (PHENIX.REFINE: 1.6.4_486) refinement
PHENIX model building
XDS data collection