X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.9
Temperature 293.0
Details 25% PEG MME 2000, 0.1M Tris-HCl , pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 33.84 α = 90
b = 107.14 β = 90
c = 288.71 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD msc saturna200 -- 2011-04-22
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1.0000 SPRING-8 BL26B2

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 50 98.6 -- -- -- -- -- 71994 2.0 2.0 19.45
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)
1.98 2.03 99.6 -- -- -- -- --

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 2.0 43.895 -- 0.09 -- 71994 3571 98.95 -- 0.1992 0.1968 0.2444 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 2.0 2.0715 -- 355 6673 0.2216 0.2955 -- 99.0
X Ray Diffraction 2.0715 2.1544 -- 338 6797 0.2056 0.2705 -- 99.0
X Ray Diffraction 2.1544 2.2525 -- 342 6828 0.1883 0.2376 -- 99.0
X Ray Diffraction 2.2525 2.3712 -- 362 6694 0.1966 0.2701 -- 99.0
X Ray Diffraction 2.3712 2.5198 -- 365 6751 0.1939 0.2462 -- 99.0
X Ray Diffraction 2.5198 2.7143 -- 356 6829 0.2063 0.2633 -- 99.0
X Ray Diffraction 2.7143 2.9874 -- 358 6856 0.207 0.2583 -- 99.0
X Ray Diffraction 2.9874 3.4195 -- 363 6933 0.1964 0.25 -- 99.0
X Ray Diffraction 3.4195 4.3077 -- 366 6952 0.1891 0.2276 -- 99.0
X Ray Diffraction 4.3077 43.9056 -- 366 7110 0.1887 0.2075 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 23.9456
Anisotropic B[1][1] -0.7812
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.0152
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.7964
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 15.333
f_plane_restr 0.005
f_chiral_restr 0.072
f_angle_d 1.09
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7635
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 721

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (phenix.refine: 1.6.4_486) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement