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, 18% PEG3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 55.14 α = 90
b = 77.63 β = 114.2
c = 54.95 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 2011-09-02
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
2.25 28 98.2 0.098 -- -- 5.7 112322 112322 0.0 -3.0 36.11
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)
2.25 2.33 99.0 0.599 -- 2.38 3.6 --

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 2.25 21.105 -- 0.0 17616 17616 1719 86.93 0.2206 0.2206 0.214 0.2818 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 2.2456 2.3115 -- 117 969 0.3698 0.4379 -- 64.0
X Ray Diffraction 2.3115 2.3861 -- 140 1267 0.2962 0.3954 -- 84.0
X Ray Diffraction 2.3861 2.4712 -- 116 1226 0.299 0.4426 -- 82.0
X Ray Diffraction 2.4712 2.57 -- 149 1274 0.2936 0.3798 -- 82.0
X Ray Diffraction 2.57 2.6867 -- 136 1272 0.2434 0.3189 -- 85.0
X Ray Diffraction 2.6867 2.8281 -- 142 1284 0.2508 0.3343 -- 85.0
X Ray Diffraction 2.8281 3.0048 -- 156 1362 0.2318 0.3222 -- 90.0
X Ray Diffraction 3.0048 3.236 -- 155 1448 0.2162 0.2923 -- 94.0
X Ray Diffraction 3.236 3.5603 -- 158 1474 0.2064 0.2566 -- 97.0
X Ray Diffraction 3.5603 4.0723 -- 133 1390 0.1645 0.257 -- 90.0
X Ray Diffraction 4.0723 5.1185 -- 145 1373 0.1558 0.1908 -- 89.0
X Ray Diffraction 5.1185 21.1055 -- 172 1558 0.223 0.2689 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_chiral_restr 0.055
f_dihedral_angle_d 19.863
f_angle_d 0.981
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2548
Nucleic Acid Atoms 635
Heterogen Atoms 34
Solvent Atoms 107

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