X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 293.0
Details 10mM Tris-HCl, 150mM NaCl, 0.2M Na/K tartrate, 20% PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 62.33 α = 90
b = 62.33 β = 90
c = 85.18 γ = 120
Symmetry
Space Group P 31

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX225HE -- 2011-06-22
Diffraction Radiation
Monochromator Protocol
Double-crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1 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
1.7 50 98.3 0.095 -- -- 3.8 40121 40121 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)
1.7 1.73 89.6 0.37 -- -- 2.2 1826

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 1.699 26.989 -- 2.11 40113 40113 2015 98.4 0.1671 0.1671 0.1654 0.203 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 1.7003 1.7428 -- 138 2531 0.2856 0.3279 -- 86.0
X Ray Diffraction 1.7428 1.79 -- 125 2640 0.2527 0.2574 -- 92.0
X Ray Diffraction 1.79 1.8426 -- 137 2692 0.2444 0.2973 -- 93.0
X Ray Diffraction 1.8426 1.9021 -- 147 2718 0.2218 0.2566 -- 93.0
X Ray Diffraction 1.9021 1.97 -- 145 2719 0.2031 0.2314 -- 94.0
X Ray Diffraction 1.97 2.0489 -- 146 2697 0.1977 0.2352 -- 94.0
X Ray Diffraction 2.0489 2.1421 -- 148 2783 0.1753 0.2104 -- 94.0
X Ray Diffraction 2.1421 2.2549 -- 138 2772 0.1783 0.2399 -- 95.0
X Ray Diffraction 2.2549 2.3961 -- 158 2762 0.1759 0.2041 -- 94.0
X Ray Diffraction 2.3961 2.5809 -- 145 2740 0.1741 0.2273 -- 95.0
X Ray Diffraction 2.5809 2.8404 -- 144 2772 0.1672 0.2203 -- 95.0
X Ray Diffraction 2.8404 3.2506 -- 141 2719 0.1603 0.1851 -- 95.0
X Ray Diffraction 3.2506 4.0926 -- 133 2759 0.1289 0.1773 -- 95.0
X Ray Diffraction 4.0926 25.1317 -- 140 2761 0.1261 0.1552 -- 95.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 31.128
Anisotropic B[1][1] 5.8668
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 5.8668
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -11.7335
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 14.588
f_plane_restr 0.003
f_chiral_restr 0.058
f_angle_d 0.92
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2547
Nucleic Acid Atoms 0
Heterogen Atoms 10
Solvent Atoms 321

Software

Computing
Computing Package Purpose
BSS Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
MOLREP Structure Solution
PHENIX (phenix.refine: 1.7.2_869) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 refinement
SCALEPACK data reduction