X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 277.0
Details 0.2 M Zn acetate, 0.1 M Na cacodylate pH 6.5, 10% isopropanol

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 76.78 α = 90
b = 113.39 β = 90
c = 140.32 γ = 90
Symmetry
Space Group I 2 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm -- 2012-02-19
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON MAX II BEAMLINE I911-2 1.041 MAX II I911-2

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
2.3 35 99.7 0.074 -- -- 7.0 -- 27554 2.0 -3.0 44.57
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)
2.3 2.36 100.0 0.435 -- 4.12 7.2 --

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 2.3 27.242 -- 2.0 -- 27064 1355 98.0 -- 0.1877 0.1866 0.2067 random selection
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 2.3 -- -- 131 2520 0.2279 0.2752 -- 97.0
X Ray Diffraction 2.3822 -- -- 127 2507 0.2188 0.2596 -- 97.0
X Ray Diffraction 2.4775 -- -- 135 2509 0.2065 0.275 -- 97.0
X Ray Diffraction 2.5902 -- -- 131 2544 0.2022 0.244 -- 98.0
X Ray Diffraction 2.7266 -- -- 136 2528 0.2045 0.2747 -- 98.0
X Ray Diffraction 2.8972 -- -- 124 2580 0.2181 0.2344 -- 99.0
X Ray Diffraction 3.1206 -- -- 145 2577 0.1944 0.1942 -- 99.0
X Ray Diffraction 3.4341 -- -- 145 2624 0.1731 0.1987 -- 99.0
X Ray Diffraction 3.9298 -- -- 143 2623 0.149 0.1606 -- 99.0
X Ray Diffraction 4.9463 27.2439 -- 138 2697 0.1934 0.1999 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 52.48
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_bond_d 0.004
f_dihedral_angle_d 14.74
f_angle_d 0.875
f_chiral_restr 0.059
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2974
Nucleic Acid Atoms 0
Heterogen Atoms 42
Solvent Atoms 186

Software

Software
Software Name Purpose
XDS data scaling
XSCALE data scaling
PDB_EXTRACT data extraction version: 3.14
PHASER phasing
PHENIX refinement version: (phenix.refine: 1.8.2_1309)