X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Liquid Diffusion
pH 6.8
Temperature 295.0
Details sodium phosphate, potassium phosphate, toluene, pH 6.8, LIQUID DIFFUSION, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 53.44 α = 90
b = 53.44 β = 90
c = 193.58 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
IMAGE PLATE RIGAKU RAXIS IV++ Osmic 2009-02-10
Diffraction Radiation
Monochromator Protocol
Osmic mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R 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 21.43 99.4 0.044 -- -- 10.29 19912 19790 2.0 2.0 --
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)
2.0 2.07 93.5 0.274 -- 5.8 7.05 1817

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 21.43 -- 1.34 19790 19738 1007 99.12 -- 0.2312 0.2291 0.2704 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 2.0 2.1054 -- 146 2492 0.2647 0.333 -- 95.0
X Ray Diffraction 2.1054 2.2371 -- 143 2619 0.2447 0.2993 -- 100.0
X Ray Diffraction 2.2371 2.4097 -- 145 2635 0.2592 0.3277 -- 100.0
X Ray Diffraction 2.4097 2.6517 -- 160 2635 0.2479 0.3103 -- 100.0
X Ray Diffraction 2.6517 3.0345 -- 130 2699 0.2447 0.2945 -- 100.0
X Ray Diffraction 3.0345 3.8197 -- 151 2739 0.2203 0.2535 -- 100.0
X Ray Diffraction 3.8197 21.43 -- 132 2912 0.2163 0.242 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 53.86
Anisotropic B[1][1] -2.4857
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.4857
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 4.9713
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.009
f_plane_restr 0.006
f_angle_d 1.231
f_chiral_restr 0.066
f_dihedral_angle_d 15.067
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2180
Nucleic Acid Atoms 0
Heterogen Atoms 96
Solvent Atoms 79

Software

Software
Software Name Purpose
CrystalClear data collection
PHASER phasing
PHENIX refinement version: (phenix.refine: 1.7.3_928)
d*TREK data reduction
d*TREK data scaling