X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 295.0
Details 4-5% isopropanol, optimised mixture of salts, 50mM Na cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 116.76 α = 90
b = 116.76 β = 90
c = 182.81 γ = 120
Symmetry
Space Group P 32

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2009-08-07
Diffraction Radiation
Monochromator Protocol
Double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 DIAMOND I03

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
3.5 50 97.7 0.065 0.065 -- 6.1 -- 34407 -3.0 0.0 134.28
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)
3.5 3.63 100.0 0.4 0.4 4.325 6.5 3529

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 3.5 29.318 -- 1.97 -- 34220 3524 97.53 -- 0.1859 0.1813 0.2257 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 3.5001 3.5479 -- 158 1269 0.2629 0.3279 -- 99.0
X Ray Diffraction 3.5479 3.5985 -- 133 1215 0.2561 0.2713 -- 99.0
X Ray Diffraction 3.5985 3.6521 -- 124 1268 0.225 0.3055 -- 99.0
X Ray Diffraction 3.6521 3.7091 -- 138 1250 0.2207 0.2481 -- 100.0
X Ray Diffraction 3.7091 3.7698 -- 162 1281 0.1961 0.2635 -- 100.0
X Ray Diffraction 3.7698 3.8347 -- 151 1207 0.1924 0.2465 -- 99.0
X Ray Diffraction 3.8347 3.9042 -- 151 1275 0.1704 0.1982 -- 100.0
X Ray Diffraction 3.9042 3.9792 -- 123 1257 0.1646 0.2185 -- 100.0
X Ray Diffraction 3.9792 4.0602 -- 143 1267 0.1656 0.2634 -- 99.0
X Ray Diffraction 4.0602 4.1482 -- 144 1233 0.1602 0.2213 -- 100.0
X Ray Diffraction 4.1482 4.2444 -- 156 1245 0.1552 0.203 -- 100.0
X Ray Diffraction 4.2444 4.3503 -- 151 1273 0.1369 0.2077 -- 100.0
X Ray Diffraction 4.3503 4.4675 -- 138 1245 0.1238 0.1661 -- 100.0
X Ray Diffraction 4.4675 4.5985 -- 169 1236 0.1168 0.1515 -- 100.0
X Ray Diffraction 4.5985 4.7463 -- 136 1235 0.1242 0.1757 -- 100.0
X Ray Diffraction 4.7463 4.9152 -- 151 1301 0.1329 0.1957 -- 100.0
X Ray Diffraction 4.9152 5.111 -- 130 1248 0.1449 0.2051 -- 100.0
X Ray Diffraction 5.111 5.3423 -- 137 1259 0.157 0.2065 -- 100.0
X Ray Diffraction 5.3423 5.622 -- 148 1276 0.1695 0.2402 -- 100.0
X Ray Diffraction 5.622 5.9715 -- 153 1233 0.1926 0.2327 -- 100.0
X Ray Diffraction 5.9715 6.4281 -- 136 1280 0.1852 0.2655 -- 100.0
X Ray Diffraction 6.4281 7.0668 -- 134 1257 0.1812 0.25 -- 100.0
X Ray Diffraction 7.0668 8.0706 -- 141 1270 0.1766 0.2066 -- 100.0
X Ray Diffraction 8.0706 10.0986 -- 134 1142 0.1816 0.1722 -- 91.0
X Ray Diffraction 10.0986 29.319 -- 83 674 0.2492 0.2467 -- 54.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic+TLS
Mean Isotropic B 147.717
Anisotropic B[1][1] -4.813
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -4.813
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -25.078
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 20.065
f_plane_restr 0.006
f_chiral_restr 0.095
f_angle_d 1.441
f_bond_d 0.027
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9865
Nucleic Acid Atoms 730
Heterogen Atoms 2
Solvent Atoms 4

Software

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