X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 291.0
Details 50 mM Tris, 1.9 M cesium chloride, 50% DMSO, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 92.4 α = 90
b = 92.4 β = 90
c = 131.2 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-225 Collimating Mirror 2010-12-14
Diffraction Radiation
Monochromator Protocol
Double Crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.2 0.91841 BESSY 14.2

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
1.44 50 99.7 -- 0.062 -- 5.0 60157 60157 -- -- --
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)
1.44 1.46 96.2 -- 0.272 5.4 4.3 2836

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 1.44 30.349 -- 0.0 61525 58574 2951 97.18 0.1429 0.1429 0.1421 0.1586 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 1.44 1.4636 -- 131 2488 0.1672 0.1758 -- 93.0
X Ray Diffraction 1.4636 1.4888 -- 123 2493 0.1792 0.2184 -- 93.0
X Ray Diffraction 1.4888 1.5159 -- 138 2508 0.1615 0.2098 -- 94.0
X Ray Diffraction 1.5159 1.5451 -- 136 2551 0.156 0.1477 -- 95.0
X Ray Diffraction 1.5451 1.5766 -- 148 2529 0.1418 0.1496 -- 95.0
X Ray Diffraction 1.5766 1.6109 -- 126 2565 0.1476 0.1923 -- 96.0
X Ray Diffraction 1.6109 1.6484 -- 114 2639 0.142 0.1594 -- 97.0
X Ray Diffraction 1.6484 1.6896 -- 134 2609 0.1364 0.1657 -- 97.0
X Ray Diffraction 1.6896 1.7353 -- 144 2606 0.1338 0.1393 -- 97.0
X Ray Diffraction 1.7353 1.7863 -- 149 2613 0.1366 0.1795 -- 97.0
X Ray Diffraction 1.7863 1.844 -- 128 2633 0.1335 0.1952 -- 97.0
X Ray Diffraction 1.844 1.9099 -- 148 2621 0.1354 0.1478 -- 97.0
X Ray Diffraction 1.9099 1.9863 -- 138 2678 0.1368 0.1561 -- 99.0
X Ray Diffraction 1.9863 2.0767 -- 140 2697 0.1425 0.1777 -- 99.0
X Ray Diffraction 2.0767 2.1862 -- 136 2720 0.1378 0.1706 -- 99.0
X Ray Diffraction 2.1862 2.3231 -- 131 2726 0.1338 0.1519 -- 99.0
X Ray Diffraction 2.3231 2.5024 -- 152 2714 0.1424 0.1494 -- 99.0
X Ray Diffraction 2.5024 2.754 -- 158 2723 0.1404 0.1573 -- 99.0
X Ray Diffraction 2.754 3.1522 -- 142 2775 0.1406 0.1406 -- 100.0
X Ray Diffraction 3.1522 3.97 -- 178 2793 0.1351 0.13 -- 100.0
X Ray Diffraction 3.97 30.3561 -- 157 2942 0.1517 0.1755 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -1.2906
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.2906
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.5811
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.074
f_dihedral_angle_d 15.128
f_angle_d 1.048
f_bond_d 0.012
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2432
Nucleic Acid Atoms 0
Heterogen Atoms 75
Solvent Atoms 477

Software

Computing
Computing Package Purpose
MAR345dtb Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7_650) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7_650) refinement
PHASER model building
MAR345dtb data collection