X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.5
Temperature 293.0
Details 20% (w/v) PEG 3000, 0.1 M sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 113.17 α = 90
b = 131.5 β = 103.17
c = 164.28 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 200
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2010-12-20
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-ID 1.00 APS 22-ID

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
2.8 50 66.6 0.159 0.159 -- 3.2 114379 76177 1.0 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)
2.8 2.9 16.7 0.353 -- 1.4 1.5 1902

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 2.821 44.209 -- 0.0 112776 71850 3586 63.71 -- 0.2233 0.2213 0.2621 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 2.8213 2.8585 -- 3 76 0.3552 0.321 -- 2.0
X Ray Diffraction 2.8585 2.8976 -- 11 219 0.3987 0.5517 -- 5.0
X Ray Diffraction 2.8976 2.939 -- 16 407 0.3487 0.4509 -- 10.0
X Ray Diffraction 2.939 2.9829 -- 42 552 0.3319 0.3872 -- 14.0
X Ray Diffraction 2.9829 3.0295 -- 30 711 0.3492 0.4132 -- 18.0
X Ray Diffraction 3.0295 3.0791 -- 47 896 0.3585 0.326 -- 22.0
X Ray Diffraction 3.0791 3.1322 -- 58 1111 0.3314 0.3873 -- 27.0
X Ray Diffraction 3.1322 3.1891 -- 73 1305 0.3231 0.3651 -- 32.0
X Ray Diffraction 3.1891 3.2505 -- 71 1588 0.3036 0.3481 -- 38.0
X Ray Diffraction 3.2505 3.3168 -- 88 1956 0.301 0.32 -- 48.0
X Ray Diffraction 3.3168 3.3889 -- 134 2364 0.3038 0.3429 -- 58.0
X Ray Diffraction 3.3889 3.4677 -- 150 2767 0.2928 0.3576 -- 67.0
X Ray Diffraction 3.4677 3.5544 -- 164 3016 0.2755 0.3235 -- 73.0
X Ray Diffraction 3.5544 3.6504 -- 162 3251 0.2603 0.3459 -- 79.0
X Ray Diffraction 3.6504 3.7578 -- 171 3467 0.2494 0.3183 -- 84.0
X Ray Diffraction 3.7578 3.879 -- 190 3647 0.228 0.2557 -- 89.0
X Ray Diffraction 3.879 4.0176 -- 221 3860 0.2156 0.2505 -- 94.0
X Ray Diffraction 4.0176 4.1783 -- 181 4044 0.1768 0.2515 -- 98.0
X Ray Diffraction 4.1783 4.3683 -- 231 4093 0.164 0.2156 -- 99.0
X Ray Diffraction 4.3683 4.5984 -- 230 4079 0.1574 0.2038 -- 99.0
X Ray Diffraction 4.5984 4.8861 -- 226 4107 0.1657 0.1892 -- 99.0
X Ray Diffraction 4.8861 5.2628 -- 200 4137 0.1698 0.2101 -- 100.0
X Ray Diffraction 5.2628 5.7914 -- 206 4121 0.2031 0.2581 -- 100.0
X Ray Diffraction 5.7914 6.627 -- 229 4133 0.2216 0.2648 -- 100.0
X Ray Diffraction 6.627 8.3402 -- 213 4151 0.2057 0.2232 -- 100.0
X Ray Diffraction 8.3402 44.2146 -- 239 4206 0.2366 0.2412 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -0.4863
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 3.0705
Anisotropic B[2][2] -1.9715
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.4578
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_chiral_restr 0.049
f_dihedral_angle_d 15.454
f_angle_d 0.856
f_bond_d 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19947
Nucleic Acid Atoms 0
Heterogen Atoms 168
Solvent Atoms 0

Software

Computing
Computing Package Purpose
SERGUI Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.6.4_486) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.6.4_486) refinement
PHASER model building
SERGUI data collection