X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
Temperature 282.0
Details Protein solution was at 12.5 mg/mL containing 20 mM Tris (pH 7.5), 100 mM NaCl, 10 mM EDTA and 10 mM bME. Mother liqueur contained 0.17 M Ammonium acetate, 0.085 M Na-citrate tribasic, dihydrate (pH 5.6), 25.5% PEG 4,000 and 15% v/v glycerol, vapor diffusion, sitting drop, temperature 282K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 155.47 α = 90
b = 113.02 β = 105.89
c = 128.59 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-300 -- 2012-02-15
Diffraction Radiation
Monochromator Protocol
C(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 APS 21-ID-G

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
2.1 30 99.5 -- 0.148 -- -- -- 118199 0.0 -3.0 23.762
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)
2.1 2.15 99.8 0.609 -- 2.44 -- --

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 2.1 29.965 -- 1.99 -- 118199 6221 99.91 0.172 0.1505 0.1486 0.1863 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 2.1 2.1239 -- 207 3939 0.1828 0.2422 -- 100.0
X Ray Diffraction 2.1239 2.1489 -- 206 3909 0.1784 0.2614 -- 100.0
X Ray Diffraction 2.1489 2.1751 -- 207 3930 0.1732 0.2252 -- 100.0
X Ray Diffraction 2.1751 2.2026 -- 205 3905 0.1697 0.2158 -- 100.0
X Ray Diffraction 2.2026 2.2315 -- 208 3950 0.1691 0.231 -- 100.0
X Ray Diffraction 2.2315 2.2621 -- 207 3928 0.1704 0.2355 -- 100.0
X Ray Diffraction 2.2621 2.2944 -- 208 3942 0.1735 0.2575 -- 100.0
X Ray Diffraction 2.2944 2.3286 -- 205 3897 0.1699 0.2385 -- 100.0
X Ray Diffraction 2.3286 2.365 -- 206 3919 0.1645 0.2266 -- 100.0
X Ray Diffraction 2.365 2.4038 -- 208 3960 0.1582 0.228 -- 100.0
X Ray Diffraction 2.4038 2.4452 -- 206 3911 0.1642 0.2259 -- 100.0
X Ray Diffraction 2.4452 2.4897 -- 206 3906 0.1592 0.2095 -- 100.0
X Ray Diffraction 2.4897 2.5375 -- 207 3947 0.1565 0.2004 -- 100.0
X Ray Diffraction 2.5375 2.5893 -- 209 3953 0.1529 0.2089 -- 100.0
X Ray Diffraction 2.5893 2.6456 -- 205 3904 0.1496 0.2091 -- 100.0
X Ray Diffraction 2.6456 2.7071 -- 205 3895 0.1557 0.2086 -- 100.0
X Ray Diffraction 2.7071 2.7747 -- 207 3940 0.1533 0.2054 -- 100.0
X Ray Diffraction 2.7747 2.8497 -- 208 3947 0.1498 0.1878 -- 100.0
X Ray Diffraction 2.8497 2.9335 -- 206 3918 0.1487 0.1908 -- 100.0
X Ray Diffraction 2.9335 3.0281 -- 208 3941 0.1538 0.2097 -- 100.0
X Ray Diffraction 3.0281 3.1362 -- 207 3943 0.1497 0.1773 -- 100.0
X Ray Diffraction 3.1362 3.2616 -- 207 3927 0.1428 0.1957 -- 100.0
X Ray Diffraction 3.2616 3.4098 -- 208 3958 0.136 0.1635 -- 100.0
X Ray Diffraction 3.4098 3.5893 -- 208 3955 0.1334 0.1549 -- 100.0
X Ray Diffraction 3.5893 3.8138 -- 209 3954 0.1245 0.1508 -- 100.0
X Ray Diffraction 3.8138 4.1076 -- 207 3949 0.1205 0.1552 -- 100.0
X Ray Diffraction 4.1076 4.5197 -- 209 3973 0.1245 0.1512 -- 100.0
X Ray Diffraction 4.5197 5.1708 -- 210 3971 0.1305 0.1219 -- 100.0
X Ray Diffraction 5.1708 6.5037 -- 209 3989 0.1587 0.1579 -- 100.0
X Ray Diffraction 6.5037 29.9678 -- 213 4043 0.1573 0.1638 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 16.293
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 13.003
f_plane_restr 0.005
f_chiral_restr 0.072
f_angle_d 1.029
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 13568
Nucleic Acid Atoms 0
Heterogen Atoms 102
Solvent Atoms 1450

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.8_1066) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Phaser molecular replacement
Xscale data reduction