X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.5
Temperature 289.0
Details 0.2M sodium acetate, 0.1M sodium citrate, 8% polyethylene glycol 4000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 128.65 α = 93.46
b = 129.94 β = 104.61
c = 135.61 γ = 104.01
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 345 mm plate -- 2008-11-05
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 1.5418 -- --

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
2.95 65.25 95.1 0.106 -- -- 2.1 -- 163752 -- -- 48.67
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)
2.95 3.11 92.9 0.407 -- 2.1 2.0 23325

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 2.95 65.218 -- 1.32 -- 163752 6055 87.12 -- 0.226 0.225 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 2.95 2.984 -- 179 8746 0.35 0.366 -- 78.0
X Ray Diffraction 2.984 3.019 -- 168 8794 0.33 0.404 -- 78.0
X Ray Diffraction 3.019 3.055 -- 238 8866 0.319 0.343 -- 80.0
X Ray Diffraction 3.055 3.094 -- 183 8945 0.31 0.357 -- 79.0
X Ray Diffraction 3.094 3.135 -- 169 9259 0.308 0.329 -- 82.0
X Ray Diffraction 3.135 3.178 -- 162 9211 0.297 0.376 -- 82.0
X Ray Diffraction 3.178 3.223 -- 188 9355 0.276 0.26 -- 83.0
X Ray Diffraction 3.223 3.271 -- 210 9312 0.283 0.311 -- 84.0
X Ray Diffraction 3.271 3.322 -- 211 9579 0.278 0.313 -- 84.0
X Ray Diffraction 3.322 3.377 -- 225 9642 0.26 0.284 -- 86.0
X Ray Diffraction 3.377 3.435 -- 174 9670 0.262 0.292 -- 86.0
X Ray Diffraction 3.435 3.497 -- 188 9755 0.271 0.308 -- 87.0
X Ray Diffraction 3.497 3.565 -- 194 9841 0.253 0.33 -- 87.0
X Ray Diffraction 3.565 3.638 -- 179 9787 0.23 0.304 -- 87.0
X Ray Diffraction 3.638 3.717 -- 183 9952 0.23 0.262 -- 88.0
X Ray Diffraction 3.717 3.803 -- 213 9905 0.228 0.269 -- 88.0
X Ray Diffraction 3.803 3.898 -- 230 9940 0.213 0.243 -- 89.0
X Ray Diffraction 3.898 4.004 -- 200 9991 0.208 0.227 -- 89.0
X Ray Diffraction 4.004 4.121 -- 213 10022 0.194 0.227 -- 89.0
X Ray Diffraction 4.121 4.254 -- 238 9983 0.197 0.211 -- 89.0
X Ray Diffraction 4.254 4.406 -- 199 10101 0.188 0.231 -- 90.0
X Ray Diffraction 4.406 4.583 -- 196 10141 0.179 0.196 -- 90.0
X Ray Diffraction 4.583 4.791 -- 197 10182 0.175 0.205 -- 90.0
X Ray Diffraction 4.791 5.044 -- 235 10212 0.171 0.238 -- 91.0
X Ray Diffraction 5.044 5.36 -- 215 10344 0.17 0.217 -- 91.0
X Ray Diffraction 5.36 5.773 -- 196 10280 0.169 0.176 -- 92.0
X Ray Diffraction 5.773 6.354 -- 226 10347 0.193 0.22 -- 92.0
X Ray Diffraction 6.354 7.272 -- 213 10514 0.199 0.232 -- 93.0
X Ray Diffraction 7.272 9.158 -- 261 10546 0.176 0.202 -- 94.0
X Ray Diffraction 9.158 65.234 -- 172 10668 0.238 0.245 -- 95.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 47.505
Anisotropic B[1][1] 0.313
Anisotropic B[1][2] 2.906
Anisotropic B[1][3] -2.991
Anisotropic B[2][2] -7.23
Anisotropic B[2][3] -3.638
Anisotropic B[3][3] 6.918
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 20.149
f_chiral_restr 0.08
f_bond_d 0.01
f_angle_d 1.24
f_plane_restr 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 53258
Nucleic Acid Atoms 0
Heterogen Atoms 260
Solvent Atoms 0

Software

Software
Software Name Purpose
MAR345dtb data collection
MOLREP phasing
PHENIX refinement version: (phenix.refine)
MOSFLM data reduction
SCALA data scaling