X-RAY DIFFRACTION Experimental Data & Validation

X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.1
Temperature 293.0
Details 20% PEG 3350, 0.1M K-Acetate, 0.1M KF, pH 6.1, Vapor diffusion, hanging drop, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 68.73 α = 90
b = 69.72 β = 90.1
c = 83.51 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 ADSC QUANTUM 4r TOROIDAL MIRROR 2006-04-27
Diffraction Radiation
Monochromator Protocol
DIAMOND (111), GE(220) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-3 0.9310 ESRF ID14-3

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
1.8 30 97.9 0.067 -- -- 6.5 -- 71943 0.0 0.0 --
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)
1.8 1.83 96.9 0.328 -- -- 6.3 3554

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 1.8 29.143 0.0 1.34 71927 71927 3686 97.53 -- 0.1349 0.1335 0.1631 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 1.8 1.8275 -- 177 3200 0.2123 0.244 -- 87.0
X Ray Diffraction 1.8275 1.8607 -- 173 3396 0.192 0.237 -- 92.0
X Ray Diffraction 1.8607 1.8964 -- 165 3410 0.1849 0.1862 -- 93.0
X Ray Diffraction 1.8964 1.9351 -- 178 3340 0.173 0.2177 -- 92.0
X Ray Diffraction 1.9351 1.9772 -- 191 3378 0.1603 0.1933 -- 92.0
X Ray Diffraction 1.9772 2.0231 -- 173 3373 0.1655 0.1897 -- 92.0
X Ray Diffraction 2.0231 2.0737 -- 200 3401 0.1498 0.1659 -- 93.0
X Ray Diffraction 2.0737 2.1297 -- 183 3401 0.1539 0.1824 -- 93.0
X Ray Diffraction 2.1297 2.1923 -- 171 3388 0.144 0.1852 -- 93.0
X Ray Diffraction 2.1923 2.263 -- 196 3439 0.1463 0.155 -- 93.0
X Ray Diffraction 2.263 2.3438 -- 197 3371 0.1429 0.1827 -- 93.0
X Ray Diffraction 2.3438 2.4375 -- 174 3417 0.14 0.1634 -- 93.0
X Ray Diffraction 2.4375 2.5482 -- 202 3415 0.1397 0.1805 -- 92.0
X Ray Diffraction 2.5482 2.6823 -- 174 3480 0.138 0.1709 -- 94.0
X Ray Diffraction 2.6823 2.85 -- 160 3455 0.1327 0.1713 -- 94.0
X Ray Diffraction 2.85 3.0695 -- 180 3456 0.1262 0.1551 -- 94.0
X Ray Diffraction 3.0695 3.3772 -- 199 3446 0.1189 0.1445 -- 93.0
X Ray Diffraction 3.3772 3.8633 -- 164 3489 0.1054 0.1317 -- 94.0
X Ray Diffraction 3.8633 4.8576 -- 185 3488 0.0906 0.1302 -- 94.0
X Ray Diffraction 4.8576 21.1263 -- 188 3528 0.123 0.1707 -- 93.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.2529
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 14.161
f_plane_restr 0.005
f_chiral_restr 0.067
f_angle_d 0.987
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5943
Nucleic Acid Atoms 0
Heterogen Atoms 16
Solvent Atoms 917

Software

Computing
Computing Package Purpose
DNA Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: dev_1223) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Phaser molecular replacement
HKL data reduction