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 = 92.7 α = 90
b = 92.7 β = 90
c = 130.1 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 108
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD Collimating mirror 2009-08-14
Diffraction Radiation
Monochromator Protocol
Bartels SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06DA 1.00 SLS X06DA

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
1.6 50 100.0 -- 0.08 -- 16.3 44226 44226 -- -- --
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)
1.6 1.63 100.0 -- 0.495 6.5 15.1 2164

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 1.6 43.662 -- 0.0 44799 42664 2135 96.65 0.1439 0.1439 0.1428 0.1657 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 1.6 1.6373 -- 129 2469 0.1731 0.1906 -- 90.0
X Ray Diffraction 1.6373 1.6782 -- 136 2525 0.1641 0.2094 -- 92.0
X Ray Diffraction 1.6782 1.7236 -- 137 2558 0.1619 0.1838 -- 93.0
X Ray Diffraction 1.7236 1.7743 -- 136 2599 0.1464 0.2057 -- 95.0
X Ray Diffraction 1.7743 1.8316 -- 134 2648 0.1391 0.1842 -- 96.0
X Ray Diffraction 1.8316 1.897 -- 135 2608 0.13 0.1707 -- 95.0
X Ray Diffraction 1.897 1.973 -- 118 2697 0.1304 0.1742 -- 96.0
X Ray Diffraction 1.973 2.0628 -- 141 2709 0.1346 0.1551 -- 98.0
X Ray Diffraction 2.0628 2.1715 -- 167 2708 0.1329 0.1597 -- 99.0
X Ray Diffraction 2.1715 2.3076 -- 146 2743 0.1383 0.1736 -- 99.0
X Ray Diffraction 2.3076 2.4857 -- 142 2747 0.1371 0.1651 -- 98.0
X Ray Diffraction 2.4857 2.7359 -- 154 2771 0.1407 0.156 -- 98.0
X Ray Diffraction 2.7359 3.1316 -- 147 2820 0.1422 0.1674 -- 99.0
X Ray Diffraction 3.1316 3.9451 -- 151 2869 0.1397 0.1459 -- 100.0
X Ray Diffraction 3.9451 43.6781 -- 162 3058 0.1533 0.1648 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -1.8873
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.8873
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.7746
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.075
f_dihedral_angle_d 14.803
f_angle_d 1.055
f_bond_d 0.012
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2428
Nucleic Acid Atoms 0
Heterogen Atoms 70
Solvent Atoms 400

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