X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 289.0
Details 0.86 sodium/potassium buffer, 0.15 M MOPS buffer, 0.02 M sodium fluoride, 0.01 M IMP, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 167.18 α = 90
b = 167.16 β = 90
c = 93.08 γ = 90
Symmetry
Space Group C 2 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2012-04-24
Diffraction Radiation
Monochromator Protocol
double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.9792 APS 19-ID

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
2.15 38.1 99.9 0.195 -- -- 7.3 71185 71185 0.0 0.0 32.6
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)
2.15 2.19 99.5 0.921 -- 2.66 6.7 3518

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 2.146 38.1 0.0 1.34 71179 71179 3606 99.69 -- 0.2114 0.2077 0.258 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 2.1466 2.1836 3357 166 3191 0.2274 0.3323 -- 90.0
X Ray Diffraction 2.1836 2.2233 -- 155 3369 0.2319 0.3007 -- 96.0
X Ray Diffraction 2.2233 2.2661 -- 192 3321 0.2217 0.2692 -- 95.0
X Ray Diffraction 2.2661 2.3123 -- 163 3362 0.2267 0.3258 -- 95.0
X Ray Diffraction 2.3123 2.3626 -- 174 3369 0.2259 0.2651 -- 95.0
X Ray Diffraction 2.3626 2.4175 -- 186 3357 0.2217 0.2946 -- 95.0
X Ray Diffraction 2.4175 2.478 -- 172 3355 0.221 0.2706 -- 95.0
X Ray Diffraction 2.478 2.5449 -- 174 3376 0.2179 0.2744 -- 95.0
X Ray Diffraction 2.5449 2.6198 -- 197 3354 0.2217 0.2197 -- 94.0
X Ray Diffraction 2.6198 2.7044 -- 199 3337 0.2138 0.2889 -- 94.0
X Ray Diffraction 2.7044 2.801 -- 197 3347 0.211 0.2684 -- 94.0
X Ray Diffraction 2.801 2.9131 -- 202 3366 0.2099 0.2976 -- 94.0
X Ray Diffraction 2.9131 3.0456 -- 176 3381 0.2042 0.24 -- 95.0
X Ray Diffraction 3.0456 3.2061 -- 190 3394 0.2057 0.2583 -- 95.0
X Ray Diffraction 3.2061 3.4068 -- 177 3380 0.1943 0.2483 -- 95.0
X Ray Diffraction 3.4068 3.6696 -- 168 3421 0.1828 0.258 -- 95.0
X Ray Diffraction 3.6696 4.0385 -- 194 3385 0.1841 0.2046 -- 95.0
X Ray Diffraction 4.0385 4.6218 -- 157 3448 0.1788 0.2199 -- 96.0
X Ray Diffraction 4.6218 5.8191 -- 195 3460 0.2029 0.2371 -- 95.0
X Ray Diffraction 5.8191 36.2902 -- 168 3599 0.2563 0.3206 -- 95.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 27.3149
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 13.556
f_plane_restr 0.003
f_chiral_restr 0.043
f_angle_d 0.707
f_bond_d 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9738
Nucleic Acid Atoms 0
Heterogen Atoms 96
Solvent Atoms 873

Software

Computing
Computing Package Purpose
SBC-collect Data Collection
HKL-3000 Data Reduction (intensity integration)
HKL-3000 Data Reduction (data scaling)
MOLREP, HKL3000 Structure Solution
PHENIX (phenix.refine: 1.8.1_1168) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
HKL data reduction