X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.9
Temperature 289.0
Details 100mM HEPES, 150mM NaCl, 8% PEG3350, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 63.72 α = 90
b = 71.53 β = 90
c = 115.53 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2012-03-09
CCD MARMOSAIC 225 mm CCD -- 2011-11-15
Diffraction Radiation
Monochromator Protocol
DCM SINGLE WAVELENGTH
DCM SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I04 0.9798 DIAMOND I04
SYNCHROTRON SSRF BEAMLINE BL17U 0.9798 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
1.97 50 99.0 -- -- -- -- 37989 37930 2.2 4.8 28.85
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)
1.97 2.0 100.0 -- -- -- -- --

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
SAD 1.969 36.725 -- 0.0 37989 37930 1918 95.49 0.1956 0.1956 0.1933 0.2365 5
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 1.9694 2.0187 -- 119 2138 0.234 0.3037 -- 85.0
X Ray Diffraction 2.0187 2.0733 -- 135 2390 0.2256 0.2559 -- 94.0
X Ray Diffraction 2.0733 2.1343 -- 133 2429 0.2176 0.2541 -- 95.0
X Ray Diffraction 2.1343 2.2031 -- 134 2384 0.2158 0.2769 -- 94.0
X Ray Diffraction 2.2031 2.2819 -- 121 2138 0.2632 0.336 -- 84.0
X Ray Diffraction 2.2819 2.3732 -- 122 2367 0.2111 0.2294 -- 93.0
X Ray Diffraction 2.3732 2.4812 -- 141 2472 0.2044 0.2379 -- 97.0
X Ray Diffraction 2.4812 2.612 -- 139 2511 0.206 0.2509 -- 98.0
X Ray Diffraction 2.612 2.7756 -- 143 2554 0.2199 0.24 -- 99.0
X Ray Diffraction 2.7756 2.9898 -- 143 2542 0.2024 0.2628 -- 99.0
X Ray Diffraction 2.9898 3.2905 -- 143 2567 0.195 0.2512 -- 99.0
X Ray Diffraction 3.2905 3.7662 -- 146 2598 0.171 0.2105 -- 100.0
X Ray Diffraction 3.7662 4.7435 -- 146 2636 0.1637 0.2086 -- 100.0
X Ray Diffraction 4.7435 36.7316 -- 153 2740 0.1838 0.2187 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 39.7091
Anisotropic B[1][1] -7.5012
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -4.422
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 11.9232
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 15.056
f_plane_restr 0.004
f_chiral_restr 0.072
f_angle_d 1.038
f_bond_d 0.021
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3840
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 380

Software

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