X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 298.0
Details 18% PEG-3350, 100 mM HEPES pH 7.55, 100mM Ca(OAc)2, 2.5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 122.64 α = 90
b = 122.64 β = 90
c = 69.92 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
STORAGE PHOSPHORS RIGAKU RAXIS IV++ OSMICS confocal optics 2005-08-29
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
2.8 30 91.2 0.06 -- -- 3.3 13622 12423 0.0 0.0 --
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)
2.8 2.85 57.4 0.216 -- 3.1 1.8 378

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 2.802 29.745 -- 1.53 13622 12411 1241 91.31 -- 0.2419 0.234 0.3134 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 2.802 2.9139 -- 101 906 0.32 0.4022 -- 68.0
X Ray Diffraction 2.9139 3.0464 -- 127 1141 0.3001 0.3529 -- 86.0
X Ray Diffraction 3.0464 3.2069 -- 131 1188 0.2713 0.3431 -- 89.0
X Ray Diffraction 3.2069 3.4075 -- 138 1235 0.2511 0.3067 -- 93.0
X Ray Diffraction 3.4075 3.6702 -- 141 1278 0.2345 0.3573 -- 95.0
X Ray Diffraction 3.6702 4.0387 -- 146 1313 0.2353 0.3393 -- 98.0
X Ray Diffraction 4.0387 4.6213 -- 147 1329 0.1882 0.3053 -- 98.0
X Ray Diffraction 4.6213 5.8152 -- 152 1366 0.2189 0.2841 -- 98.0
X Ray Diffraction 5.8152 29.7467 -- 158 1414 0.2359 0.2842 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 11.3924
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 11.3924
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -22.7848
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.007
f_chiral_restr 0.08
f_dihedral_angle_d 18.532
f_angle_d 1.213
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2673
Nucleic Acid Atoms 325
Heterogen Atoms 0
Solvent Atoms 0

Software

Computing
Computing Package Purpose
CrystalClear Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASER in PHENIX Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.3_928) refinement
PHASER version: in PHENIX model building
CrystalClear data collection