X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 6.2
Temperature 298.0
Details Purified enzyme was concentrated to ~8 mg/mL and then added into a crystallization screen containing 0.1 M tri-sodium citrate pH=5.6, 24-34% PEG 4K, and 0.1-0.25 M ammonium acetate. 1.5L of protein solution was added to each well and mixed with an equivalent volume of reservoir solution., pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 57.6 α = 90
b = 57.6 β = 90
c = 122.4 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2012-06-15
Diffraction Radiation
Monochromator Protocol
DOUBLE CRYSTAL, SI(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.2.1 -- ALS 8.2.1

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
1.45 34 88.2 -- -- -- -- -- 33886 -- 0.0 --

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 1.45 33.91 -- 1.33 -- 32889 3202 87.9 -- 0.154 0.149 0.199 --
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 1.45 1.4716 -- 74 701 0.3524 0.3946 -- 48.0
X Ray Diffraction 1.4716 1.4946 -- 123 1259 0.3169 0.3714 -- 88.0
X Ray Diffraction 1.4946 1.5191 -- 101 965 0.319 0.3571 -- 66.0
X Ray Diffraction 1.5191 1.5453 -- 135 1310 0.2741 0.368 -- 92.0
X Ray Diffraction 1.5453 1.5734 -- 177 1424 0.2297 0.3165 -- 100.0
X Ray Diffraction 1.5734 1.6037 -- 171 1416 0.1931 0.2847 -- 100.0
X Ray Diffraction 1.6037 1.6364 -- 144 1455 0.1792 0.2397 -- 100.0
X Ray Diffraction 1.6364 1.672 -- 166 1434 0.1642 0.2383 -- 100.0
X Ray Diffraction 1.672 1.7109 -- 147 1237 0.1613 0.2541 -- 86.0
X Ray Diffraction 1.7109 1.7537 -- 134 1323 0.1526 0.2501 -- 91.0
X Ray Diffraction 1.7537 1.8011 -- 160 1449 0.1362 0.2704 -- 100.0
X Ray Diffraction 1.8011 1.8541 -- 137 1478 0.1406 0.2556 -- 100.0
X Ray Diffraction 1.8541 1.9139 -- 108 999 0.1705 0.2909 -- 69.0
X Ray Diffraction 1.9139 1.9823 -- 112 1019 0.1362 0.2189 -- 69.0
X Ray Diffraction 1.9823 2.0617 -- 146 1276 0.1245 0.2047 -- 89.0
X Ray Diffraction 2.0617 2.1555 -- 139 1294 0.1262 0.1903 -- 89.0
X Ray Diffraction 2.1555 2.2691 -- 106 1109 0.1251 0.1969 -- 75.0
X Ray Diffraction 2.2691 2.4113 -- 136 1510 0.1355 0.1894 -- 100.0
X Ray Diffraction 2.4113 2.5974 -- 173 1461 0.1409 0.2017 -- 100.0
X Ray Diffraction 2.5974 2.8587 -- 140 1244 0.1454 0.2248 -- 84.0
X Ray Diffraction 2.8587 3.272 -- 169 1499 0.1431 0.1721 -- 100.0
X Ray Diffraction 3.272 4.1213 -- 126 1192 0.1339 0.1489 -- 77.0
X Ray Diffraction 4.1213 33.9162 -- 178 1633 0.1539 0.1661 -- 100.0
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.014
f_dihedral_angle_d 14.359
f_angle_d 1.296
f_chiral_restr 0.083
f_plane_restr 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1512
Nucleic Acid Atoms 0
Heterogen Atoms 8
Solvent Atoms 256

Software

Software
Software Name Purpose
ADSC data collection version: Quantum
PHENIX model building version: (phenix.refine: 1.8_1069)
PHENIX refinement version: (phenix.refine: 1.8_1069)
MOSFLM data reduction
SCALA data scaling
PHENIX phasing version: 1.8_1069