X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 277.0
Details 0.025 M Bicine pH 8.5, 0.25 M NaCl, 20% glycerol, vapor diffusion, hanging drop, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 50.5 α = 90
b = 103.85 β = 90.02
c = 70 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
CCD ADSC QUANTUM 315r -- 2009-10-28
Diffraction Radiation
Monochromator Protocol
Double-crystal, Si(111) SINGLE
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 5.0.1 0.979 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
1.95 50.5 98.7 -- 0.069 -- 3.5 52039 52039 0.0 0.0 19.0
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)
1.948 2.05 96.6 0.357 0.357 2.1 2.9 7369

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 1.948 50.502 0.0 1.38 52039 51908 2642 98.43 -- 0.189 0.1864 0.2341 --
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 1.948 1.9832 -- 131 2435 0.2385 0.28 -- 89.0
X Ray Diffraction 1.9832 2.0213 -- 120 2592 0.2187 0.2915 -- 93.0
X Ray Diffraction 2.0213 2.0626 -- 136 2569 0.2121 0.2677 -- 93.0
X Ray Diffraction 2.0626 2.1074 -- 131 2571 0.2285 0.2866 -- 93.0
X Ray Diffraction 2.1074 2.1564 -- 143 2605 0.2052 0.235 -- 94.0
X Ray Diffraction 2.1564 2.2103 -- 151 2598 0.1989 0.2402 -- 94.0
X Ray Diffraction 2.2103 2.27 -- 137 2476 0.258 0.3325 -- 90.0
X Ray Diffraction 2.27 2.3367 -- 137 2546 0.21 0.2885 -- 92.0
X Ray Diffraction 2.3367 2.4121 -- 140 2657 0.1962 0.2291 -- 95.0
X Ray Diffraction 2.4121 2.4983 -- 131 2597 0.1876 0.2352 -- 95.0
X Ray Diffraction 2.4983 2.5982 -- 140 2594 0.1869 0.2566 -- 94.0
X Ray Diffraction 2.5982 2.7163 -- 125 2630 0.1801 0.2561 -- 95.0
X Ray Diffraction 2.7163 2.8593 -- 149 2605 0.1747 0.2283 -- 94.0
X Ray Diffraction 2.8593 3.0382 -- 144 2658 0.1715 0.219 -- 95.0
X Ray Diffraction 3.0382 3.2723 -- 125 2579 0.1683 0.201 -- 94.0
X Ray Diffraction 3.2723 3.6008 -- 127 2685 0.1541 0.2152 -- 95.0
X Ray Diffraction 3.6008 4.1199 -- 166 2548 0.1564 0.2066 -- 92.0
X Ray Diffraction 4.1199 5.1832 -- 146 2627 0.1651 0.2048 -- 94.0
X Ray Diffraction 5.1832 25.2531 -- 130 2696 0.2144 0.2423 -- 95.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 28.2179
Anisotropic B[1][1] -4.4851
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.7509
Anisotropic B[2][2] 5.8547
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.3696
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 17.13
f_bond_d 0.02
f_chiral_restr 0.138
f_angle_d 1.92
f_plane_restr 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4915
Nucleic Acid Atoms 0
Heterogen Atoms 50
Solvent Atoms 183

Software

Software
Software Name Purpose
d*TREK data scaling
SCALA data scaling version: 3.3.20
PHASER phasing
PHENIX refinement version: dev_991
PDB_EXTRACT data extraction version: 3.10
CBASS data collection
d*TREK data reduction