X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Evaporation
pH 7.5
Temperature 298.0
Details 10 % PEG3350, 0.4M NH4SO4, 1% JM600, 5% Glycerol, 0.1M Bis-tris propane (7.5), EVAPORATION, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 160.27 α = 90
b = 160.27 β = 90
c = 682.84 γ = 120
Symmetry
Space Group H 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2010-04-09
Diffraction Radiation
Monochromator Protocol
Cryo-Cooled Si(111) double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 0.9792 APS 24-ID-C

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
2.9 39.5 93.2 0.09 -- -- 1.4 -- 75498 3.0 3.0 --
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)
2.898 3.0 90.9 0.493 -- 1.5 1.5 --

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 2.898 39.493 -- 0.09 -- 59612 2975 78.93 -- 0.231 0.229 0.267 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 2.898 2.945 -- 84 2066 0.368 0.428 -- 61.0
X Ray Diffraction 2.945 2.996 -- 110 2170 0.355 0.366 -- 64.0
X Ray Diffraction 2.996 3.051 -- 97 2151 0.346 0.395 -- 63.0
X Ray Diffraction 3.051 3.109 -- 112 2222 0.33 0.384 -- 66.0
X Ray Diffraction 3.109 3.173 -- 122 2288 0.314 0.36 -- 68.0
X Ray Diffraction 3.173 3.242 -- 154 2339 0.293 0.308 -- 70.0
X Ray Diffraction 3.242 3.317 -- 118 2428 0.285 0.374 -- 71.0
X Ray Diffraction 3.317 3.4 -- 128 2538 0.274 0.314 -- 75.0
X Ray Diffraction 3.4 3.492 -- 153 2561 0.261 0.307 -- 76.0
X Ray Diffraction 3.492 3.595 -- 118 2655 0.258 0.285 -- 78.0
X Ray Diffraction 3.595 3.711 -- 147 2688 0.244 0.313 -- 79.0
X Ray Diffraction 3.711 3.843 -- 141 2748 0.231 0.283 -- 81.0
X Ray Diffraction 3.843 3.997 -- 145 2825 0.216 0.279 -- 83.0
X Ray Diffraction 3.997 4.179 -- 154 2857 0.191 0.222 -- 85.0
X Ray Diffraction 4.179 4.399 -- 171 2909 0.175 0.23 -- 85.0
X Ray Diffraction 4.399 4.674 -- 149 3035 0.163 0.213 -- 88.0
X Ray Diffraction 4.674 5.034 -- 160 3089 0.158 0.181 -- 90.0
X Ray Diffraction 5.034 5.539 -- 170 3143 0.182 0.243 -- 91.0
X Ray Diffraction 5.539 6.338 -- 174 3181 0.208 0.225 -- 92.0
X Ray Diffraction 6.338 7.975 -- 174 3222 0.209 0.242 -- 92.0
X Ray Diffraction 7.975 39.496 -- 194 3522 0.211 0.224 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 69.29
Anisotropic B[1][1] 3.572
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 3.572
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -7.143
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 17.223
f_plane_restr 0.003
f_chiral_restr 0.046
f_angle_d 0.683
f_bond_d 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 12854
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 19

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
HKL Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.100 data extraction
phenix refinement
Phaser molecular replacement
SCALEPACK data scaling