X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 298.0
Details 2.3-2.9M SODIUM FORMATE, 3% PEG 4000, PH 7.6-8.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 153.12 α = 90
b = 153.12 β = 90
c = 125.11 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2010-01-07
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRF BEAMLINE BL17U 0.9792 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
3.3 50 99.5 -- -- -- 5.9 -- 25746 2.8 21.1 102.0
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)
3.3 3.42 100.0 -- -- -- -- --

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 3.3 36.62 -- 1.35 -- 25719 1451 99.6 -- 0.233 0.23 0.27 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 3.301 3.4189 -- 415 2145 0.3101 0.3736 -- 100.0
X Ray Diffraction 3.4189 3.5557 -- 0 2531 0.2853 0.0 -- 100.0
X Ray Diffraction 3.5557 3.7174 -- 0 2557 0.2543 0.0 -- 100.0
X Ray Diffraction 3.7174 3.9132 -- 343 2183 0.2461 0.3058 -- 100.0
X Ray Diffraction 3.9132 4.158 -- 0 2561 0.2288 0.0 -- 100.0
X Ray Diffraction 4.158 4.4785 -- 316 2251 0.1988 0.227 -- 100.0
X Ray Diffraction 4.4785 4.9283 -- 0 2575 0.1807 0.0 -- 100.0
X Ray Diffraction 4.9283 5.6392 -- 0 2589 0.2165 0.0 -- 100.0
X Ray Diffraction 5.6392 7.0963 -- 239 2355 0.3177 0.4145 -- 100.0
X Ray Diffraction 7.0963 36.6257 -- 138 2521 0.2113 0.1855 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 151.341
Anisotropic B[1][1] 10.7354
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 10.7354
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -21.4708
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_chiral_restr 0.065
f_dihedral_angle_d 18.327
f_angle_d 0.934
f_bond_d 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6233
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 0

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASES Structure Solution
PHENIX (PHENIX.REFINE: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
PHENIX version: (PHENIX.REFINE: 1.7.1_743) refinement
PHASES model building
HKL-2000 data collection