X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 8.5
Temperature 277.0
Details 100 mM Tris, 20% w/v PEG10000, pH 8.5, VAPOR DIFFUSION, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 40.4 α = 90
b = 117.08 β = 90
c = 118.2 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2012-11-20
Diffraction Radiation
Monochromator Protocol
Rosenbaum-Rock double-crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-ID 1.000 APS 22-ID

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
1.85 50 99.4 0.063 -- -- 3.8 49053 48759 1.0 1.0 25.07
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)
1.848 1.92 98.5 0.436 -- -- 3.3 4747

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 1.848 32.687 -- 1.35 49053 48675 2457 99.37 -- 0.1642 0.1625 0.1964 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 1.848 1.884 -- 120 2475 0.2194 0.2597 -- 97.0
X Ray Diffraction 1.884 1.9224 -- 131 2590 0.2066 0.2381 -- 100.0
X Ray Diffraction 1.9224 1.9642 -- 133 2484 0.1994 0.2444 -- 100.0
X Ray Diffraction 1.9642 2.0099 -- 145 2542 0.1843 0.2365 -- 100.0
X Ray Diffraction 2.0099 2.0602 -- 152 2526 0.1782 0.2195 -- 100.0
X Ray Diffraction 2.0602 2.1159 -- 141 2540 0.1701 0.2192 -- 100.0
X Ray Diffraction 2.1159 2.1781 -- 120 2556 0.1685 0.1944 -- 100.0
X Ray Diffraction 2.1781 2.2484 -- 138 2590 0.1685 0.2247 -- 100.0
X Ray Diffraction 2.2484 2.3287 -- 130 2510 0.1688 0.2134 -- 100.0
X Ray Diffraction 2.3287 2.422 -- 124 2578 0.1747 0.2605 -- 100.0
X Ray Diffraction 2.422 2.5321 -- 153 2568 0.1732 0.2142 -- 100.0
X Ray Diffraction 2.5321 2.6656 -- 142 2548 0.1789 0.222 -- 100.0
X Ray Diffraction 2.6656 2.8325 -- 138 2547 0.1779 0.2271 -- 99.0
X Ray Diffraction 2.8325 3.0511 -- 139 2579 0.1803 0.2162 -- 99.0
X Ray Diffraction 3.0511 3.3578 -- 117 2623 0.1519 0.165 -- 99.0
X Ray Diffraction 3.3578 3.8431 -- 132 2584 0.1384 0.1799 -- 99.0
X Ray Diffraction 3.8431 4.8393 -- 161 2617 0.1277 0.1532 -- 99.0
X Ray Diffraction 4.8393 32.6919 -- 141 2761 0.1673 0.1771 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 29.3702
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 19.889
f_plane_restr 0.004
f_chiral_restr 0.066
f_angle_d 1.099
f_bond_d 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2944
Nucleic Acid Atoms 824
Heterogen Atoms 48
Solvent Atoms 501

Software

Computing
Computing Package Purpose
SER-gui Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.8.2_1309) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
SCALEPACK data reduction
DENZO data collection