X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 293.0
Details 0.1M Tris-HCl, 2.9-3.3M sodium formate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 69.22 α = 90
b = 69.22 β = 90
c = 143.18 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
CCD RAYONIX MX225HE -- 2011-04-25
Diffraction Radiation
Monochromator Protocol
Si double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.000 SPring-8 BL41XU

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
2.1 50 98.9 -- 0.08 -- 12.1 20923 20923 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)
2.099 2.14 98.2 -- -- 2.0 12.4 994

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 2.099 40.404 -- 1.36 -- 20901 1946 99.35 -- 0.1775 0.1748 0.233 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 2.0994 2.1519 -- 143 2582 0.2841 0.3168 -- 99.0
X Ray Diffraction 2.1519 2.2101 -- 125 2615 0.2492 0.2678 -- 99.0
X Ray Diffraction 2.2101 2.2751 -- 144 2598 0.2259 0.2554 -- 99.0
X Ray Diffraction 2.2751 2.3486 -- 151 2570 0.2147 0.2714 -- 99.0
X Ray Diffraction 2.3486 2.4325 -- 158 2590 0.1913 0.2373 -- 99.0
X Ray Diffraction 2.4325 2.5299 -- 143 2612 0.1867 0.209 -- 99.0
X Ray Diffraction 2.5299 2.645 -- 157 2632 0.1942 0.2638 -- 99.0
X Ray Diffraction 2.645 2.7844 -- 133 2602 0.1906 0.2572 -- 99.0
X Ray Diffraction 2.7844 2.9588 -- 154 2610 0.1867 0.248 -- 99.0
X Ray Diffraction 2.9588 3.1872 -- 130 2635 0.1774 0.277 -- 100.0
X Ray Diffraction 3.1872 3.5078 -- 134 2634 0.1686 0.2224 -- 100.0
X Ray Diffraction 3.5078 4.0149 -- 121 2633 0.155 0.2082 -- 100.0
X Ray Diffraction 4.0149 5.0569 -- 143 2636 0.1371 0.216 -- 100.0
X Ray Diffraction 5.0569 40.4114 -- 110 2665 0.1735 0.2043 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 49.7192
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 16.465
f_bond_d 0.008
f_plane_restr 0.005
f_angle_d 1.054
f_chiral_restr 0.045
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2211
Nucleic Acid Atoms 0
Heterogen Atoms 25
Solvent Atoms 110

Software

Software
Software Name Purpose
HKL-2000 data collection
PHASER phasing
PHENIX refinement version: (phenix.refine: 1.8.1_1168)
HKL-2000 data reduction
HKL-2000 data scaling