X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 289.0
Details 0.16 M ammonium sulfate, 0.08 M sodium acetate, pH 4.6, 20% (w/v) PEG 4000, and 20% (v/v) glycerol and directly frozen , VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 53.75 α = 90.01
b = 113.89 β = 90.49
c = 122.6 γ = 90
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD NOIR-1 -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 4.2.2 1.00 ALS 4.2.2

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
2.93 49.07 98.4 0.108 -- -- 1.98 -- 61473 1.5 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)
2.93 3.03 98.3 0.438 -- 1.6 1.98 6165

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 2.93 45.303 -- 1.96 -- 61310 3069 98.15 -- 0.1935 0.1907 0.2474 --
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 2.93 2.9758 -- 130 2667 0.3199 0.3808 -- 98.0
X Ray Diffraction 2.9758 3.0246 -- 122 2596 0.3063 0.3725 -- 98.0
X Ray Diffraction 3.0246 3.0767 -- 142 2677 0.3008 0.4297 -- 98.0
X Ray Diffraction 3.0767 3.1327 -- 136 2658 0.2837 0.3564 -- 98.0
X Ray Diffraction 3.1327 3.1929 -- 153 2626 0.2617 0.3178 -- 98.0
X Ray Diffraction 3.1929 3.2581 -- 145 2616 0.2539 0.378 -- 98.0
X Ray Diffraction 3.2581 3.3289 -- 145 2670 0.2426 0.3192 -- 98.0
X Ray Diffraction 3.3289 3.4063 -- 147 2652 0.2428 0.3091 -- 98.0
X Ray Diffraction 3.4063 3.4914 -- 145 2633 0.2201 0.2714 -- 98.0
X Ray Diffraction 3.4914 3.5858 -- 148 2694 0.2186 0.3103 -- 99.0
X Ray Diffraction 3.5858 3.6913 -- 136 2608 0.2066 0.262 -- 98.0
X Ray Diffraction 3.6913 3.8104 -- 100 2750 0.1845 0.2256 -- 98.0
X Ray Diffraction 3.8104 3.9465 -- 154 2584 0.179 0.2496 -- 98.0
X Ray Diffraction 3.9465 4.1044 -- 136 2666 0.1645 0.223 -- 98.0
X Ray Diffraction 4.1044 4.291 -- 158 2614 0.1529 0.21 -- 99.0
X Ray Diffraction 4.291 4.5171 -- 136 2699 0.1449 0.1875 -- 98.0
X Ray Diffraction 4.5171 4.7998 -- 143 2632 0.1395 0.1792 -- 99.0
X Ray Diffraction 4.7998 5.1699 -- 144 2675 0.1443 0.1912 -- 99.0
X Ray Diffraction 5.1699 5.6893 -- 153 2622 0.1508 0.2162 -- 99.0
X Ray Diffraction 5.6893 6.5105 -- 135 2673 0.1645 0.2212 -- 99.0
X Ray Diffraction 6.5105 8.1946 -- 131 2658 0.1594 0.1836 -- 98.0
X Ray Diffraction 8.1946 45.3085 -- 130 2571 0.1583 0.173 -- 95.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 37.7811
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 15.788
f_plane_restr 0.007
f_chiral_restr 0.052
f_angle_d 1.187
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 14740
Nucleic Acid Atoms 3928
Heterogen Atoms 111
Solvent Atoms 408

Software

Computing
Computing Package Purpose
BLU-ICE Data Collection
DTREK Data Reduction (intensity integration)
DTREK Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (phenix.refine: 1.8.2_1309) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
D*trek version: 9.9.9.1L data reduction
D*trek data collection