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 25%(w/v) PEG 2000 monomethyl ether, 200mM magnesium chloride, 100mM sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 69.85 α = 90
b = 88.57 β = 90
c = 97.96 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 ADSC QUANTUM 315r -- --
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRF BEAMLINE BL17U 1.00000 SSRF BL17U

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
1.7 30.84 99.1 -- -- -- -- -- 33559 2.0 2.0 21.6

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 1.703 30.839 -- 1.34 -- 33245 2000 98.89 -- 0.1957 0.1943 0.2179 --
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 1.7028 1.7453 -- 139 2173 0.2305 0.2496 -- 97.0
X Ray Diffraction 1.7453 1.7925 -- 142 2208 0.2261 0.2524 -- 100.0
X Ray Diffraction 1.7925 1.8453 -- 142 2229 0.2082 0.2505 -- 100.0
X Ray Diffraction 1.8453 1.9048 -- 143 2224 0.2033 0.2464 -- 100.0
X Ray Diffraction 1.9048 1.9729 -- 144 2248 0.1973 0.2194 -- 100.0
X Ray Diffraction 1.9729 2.0519 -- 142 2217 0.1996 0.2468 -- 100.0
X Ray Diffraction 2.0519 2.1452 -- 143 2241 0.1867 0.2266 -- 100.0
X Ray Diffraction 2.1452 2.2583 -- 144 2253 0.1879 0.1946 -- 100.0
X Ray Diffraction 2.2583 2.3998 -- 144 2241 0.1974 0.239 -- 100.0
X Ray Diffraction 2.3998 2.585 -- 144 2252 0.203 0.2251 -- 100.0
X Ray Diffraction 2.585 2.8451 -- 143 2238 0.2116 0.2102 -- 100.0
X Ray Diffraction 2.8451 3.2565 -- 145 2267 0.2123 0.2022 -- 99.0
X Ray Diffraction 3.2565 4.1018 -- 143 2240 0.1796 0.2158 -- 98.0
X Ray Diffraction 4.1018 34.948 -- 142 2214 0.1765 0.2049 -- 92.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 25.3143
Anisotropic B[1][1] -2.5342
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 3.3883
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.8541
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.007
f_angle_d 1.093
f_dihedral_angle_d 14.312
f_plane_restr 0.004
f_chiral_restr 0.075
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1635
Nucleic Acid Atoms 0
Heterogen Atoms 30
Solvent Atoms 108

Software

Software
Software Name Purpose
HKL-2000 data collection
PHENIX model building
PHENIX refinement version: (phenix.refine: 1.8.1_1168)
HKL-2000 data reduction
HKL-2000 data scaling
PHENIX phasing