X-RAY DIFFRACTION Experimental Data & Validation


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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 = 54.38 α = 90
b = 79.24 β = 105.49
c = 54.88 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 2011-09-25
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
1.85 28 99.7 0.049 -- -- 4.9 185280 185280 0.0 -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)
1.85 1.92 97.2 0.367 -- 2.34 2.2 --

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 1.85 22.109 -- 0.0 36292 36292 3663 93.86 -- 0.2071 0.2028 0.2452 --
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 1.8445 1.8688 -- 74 613 0.2567 0.3213 -- 47.0
X Ray Diffraction 1.8688 1.8944 -- 121 1086 0.2624 0.3591 -- 80.0
X Ray Diffraction 1.8944 1.9214 -- 122 1094 0.2545 0.3075 -- 84.0
X Ray Diffraction 1.9214 1.9501 -- 133 1190 0.2312 0.314 -- 88.0
X Ray Diffraction 1.9501 1.9805 -- 130 1172 0.23 0.2737 -- 90.0
X Ray Diffraction 1.9805 2.013 -- 143 1228 0.235 0.2681 -- 92.0
X Ray Diffraction 2.013 2.0477 -- 139 1251 0.2128 0.2888 -- 95.0
X Ray Diffraction 2.0477 2.0849 -- 143 1310 0.2212 0.2851 -- 97.0
X Ray Diffraction 2.0849 2.1249 -- 149 1269 0.2175 0.2733 -- 97.0
X Ray Diffraction 2.1249 2.1683 -- 138 1300 0.2189 0.2868 -- 97.0
X Ray Diffraction 2.1683 2.2154 -- 142 1296 0.2161 0.2934 -- 97.0
X Ray Diffraction 2.2154 2.2669 -- 146 1320 0.2089 0.2825 -- 97.0
X Ray Diffraction 2.2669 2.3235 -- 162 1241 0.2121 0.2649 -- 98.0
X Ray Diffraction 2.3235 2.3862 -- 148 1320 0.2188 0.2827 -- 98.0
X Ray Diffraction 2.3862 2.4564 -- 126 1333 0.2189 0.2614 -- 97.0
X Ray Diffraction 2.4564 2.5356 -- 133 1310 0.2321 0.3172 -- 97.0
X Ray Diffraction 2.5356 2.626 -- 150 1280 0.2359 0.2719 -- 97.0
X Ray Diffraction 2.626 2.731 -- 160 1313 0.2133 0.281 -- 98.0
X Ray Diffraction 2.731 2.855 -- 148 1316 0.2188 0.2486 -- 98.0
X Ray Diffraction 2.855 3.0052 -- 160 1319 0.2224 0.2743 -- 99.0
X Ray Diffraction 3.0052 3.193 -- 167 1298 0.2155 0.2555 -- 99.0
X Ray Diffraction 3.193 3.4387 -- 149 1343 0.2096 0.2416 -- 100.0
X Ray Diffraction 3.4387 3.7832 -- 138 1326 0.1899 0.2192 -- 100.0
X Ray Diffraction 3.7832 4.327 -- 135 1373 0.1618 0.2319 -- 100.0
X Ray Diffraction 4.327 5.4382 -- 159 1351 0.172 0.188 -- 100.0
X Ray Diffraction 5.4382 22.1104 -- 148 1377 0.1901 0.1838 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Restrained
Anisotropic B[1][1] 2.4138
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 5.4155
Anisotropic B[2][2] -3.1888
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.775
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_chiral_restr 0.101
f_dihedral_angle_d 20.258
f_angle_d 1.231
f_bond_d 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2580
Nucleic Acid Atoms 632
Heterogen Atoms 33
Solvent Atoms 292

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