X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 298.0
Details 50 mM MES pH 6.0, 200 mM LiSO4, and 25% mPEG 2K, vapor diffusion, hanging drop, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 104.64 α = 90
b = 74.09 β = 111.98
c = 112.14 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
-- -- -- 2001-07
Diffraction Radiation
Monochromator Protocol
-- single wavelength
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 5.0.1 0.97956 ALS 5.0.1

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
2.39 30 90.05 -- -- -- -- -- 56727 -- -- --

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 2.3936 29.643 -- 1.34 -- 56705 2868 90.01 -- 0.2099 0.2079 0.2462 --
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 2.3936 2.4348 -- 132 2555 0.2854 0.3756 -- 86.0
X Ray Diffraction 2.4348 2.4791 -- 155 2630 0.2724 0.3432 -- 89.0
X Ray Diffraction 2.4791 2.5267 -- 129 2658 0.2772 0.3347 -- 89.0
X Ray Diffraction 2.5267 2.5783 -- 140 2638 0.2698 0.3405 -- 89.0
X Ray Diffraction 2.5783 2.6343 -- 165 2607 0.259 0.3228 -- 88.0
X Ray Diffraction 2.6343 2.6955 -- 134 2620 0.2532 0.2942 -- 88.0
X Ray Diffraction 2.6955 2.7629 -- 150 2577 0.2617 0.3414 -- 87.0
X Ray Diffraction 2.7629 2.8376 -- 125 2616 0.254 0.2781 -- 87.0
X Ray Diffraction 2.8376 2.921 -- 138 2575 0.2556 0.3164 -- 87.0
X Ray Diffraction 2.921 3.0152 -- 138 2576 0.2527 0.3418 -- 87.0
X Ray Diffraction 3.0152 3.1228 -- 147 2626 0.2463 0.2939 -- 87.0
X Ray Diffraction 3.1228 3.2477 -- 121 2585 0.2339 0.2514 -- 87.0
X Ray Diffraction 3.2477 3.3953 -- 134 2617 0.2206 0.2781 -- 87.0
X Ray Diffraction 3.3953 3.5741 -- 142 2620 0.207 0.2463 -- 88.0
X Ray Diffraction 3.5741 3.7976 -- 151 2676 0.1976 0.2365 -- 90.0
X Ray Diffraction 3.7976 4.0901 -- 143 2770 0.1886 0.2291 -- 92.0
X Ray Diffraction 4.0901 4.5004 -- 147 2852 0.1756 0.1971 -- 95.0
X Ray Diffraction 4.5004 5.1487 -- 154 2974 0.1759 0.2031 -- 98.0
X Ray Diffraction 5.1487 6.4756 -- 166 3001 0.1835 0.2161 -- 99.0
X Ray Diffraction 6.4756 29.6451 -- 157 3064 0.1678 0.1741 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 54.8586
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_chiral_restr 0.047
f_dihedral_angle_d 19.512
f_angle_d 0.918
f_bond_d 0.017
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8809
Nucleic Acid Atoms 1697
Heterogen Atoms 16
Solvent Atoms 272

Software

Computing
Computing Package Purpose
HKL Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
PHENIX (phenix.refine: 1.8_1069) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
AMORE molecular replacement
SCALEPACK data reduction