X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8
Temperature 291.0
Details 50mM Imidazole, 350mM Sodium Acetate, 19% PEG3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.48 α = 90
b = 78.92 β = 106.61
c = 55.13 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU SATURN 92 Mirrors 2011-05-03
Diffraction Radiation
Monochromator Protocol
mirrors VarimaxHF SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54178 -- --

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 28 99.6 0.056 -- -- 5.7 151838 151838 0.0 -3.0 30.93
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)
2.0 2.07 98.1 0.379 -- 2.8 3.1 --

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 2.0 22.572 -- 0.0 28802 28802 2890 94.8 0.2096 0.2096 0.2032 0.2673 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 1.9977 2.0304 -- 122 1107 0.2415 0.3087 -- 86.0
X Ray Diffraction 2.0304 2.0654 -- 135 1177 0.2358 0.3033 -- 91.0
X Ray Diffraction 2.0654 2.103 -- 123 1243 0.2225 0.2857 -- 95.0
X Ray Diffraction 2.103 2.1434 -- 139 1226 0.2168 0.2415 -- 95.0
X Ray Diffraction 2.1434 2.1871 -- 140 1286 0.2088 0.2994 -- 97.0
X Ray Diffraction 2.1871 2.2346 -- 126 1215 0.2241 0.2871 -- 95.0
X Ray Diffraction 2.2346 2.2865 -- 140 1215 0.2415 0.3195 -- 94.0
X Ray Diffraction 2.2865 2.3437 -- 160 1199 0.248 0.3486 -- 94.0
X Ray Diffraction 2.3437 2.407 -- 122 1230 0.264 0.3586 -- 94.0
X Ray Diffraction 2.407 2.4777 -- 113 1196 0.254 0.3433 -- 91.0
X Ray Diffraction 2.4777 2.5576 -- 136 1188 0.276 0.4152 -- 92.0
X Ray Diffraction 2.5576 2.6488 -- 138 1205 0.2491 0.358 -- 93.0
X Ray Diffraction 2.6488 2.7547 -- 144 1213 0.2237 0.276 -- 93.0
X Ray Diffraction 2.7547 2.8799 -- 132 1171 0.2242 0.3023 -- 92.0
X Ray Diffraction 2.8799 3.0314 -- 158 1219 0.2288 0.3144 -- 94.0
X Ray Diffraction 3.0314 3.2208 -- 156 1259 0.2154 0.2715 -- 98.0
X Ray Diffraction 3.2208 3.4686 -- 144 1313 0.2017 0.2694 -- 100.0
X Ray Diffraction 3.4686 3.8162 -- 132 1302 0.1839 0.2566 -- 100.0
X Ray Diffraction 3.8162 4.3649 -- 142 1312 0.1537 0.206 -- 99.0
X Ray Diffraction 4.3649 5.4863 -- 148 1293 0.1637 0.2101 -- 99.0
X Ray Diffraction 5.4863 22.5732 -- 140 1343 0.1859 0.2102 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Restrained
Mean Isotropic B 30.93
Anisotropic B[1][1] 1.8542
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 1.3066
Anisotropic B[2][2] 1.8518
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.706
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.064
f_dihedral_angle_d 20.786
f_angle_d 1.057
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2537
Nucleic Acid Atoms 633
Heterogen Atoms 31
Solvent Atoms 282

Software

Computing
Computing Package Purpose
StructureStudio Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
CNS Structure Solution
PHENIX (phenix.refine: 1.7_650) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7_650) refinement
CNS model building
StructureStudio data collection