X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 291.0
Details 100mM Sodium cacodylate 6.5, 25% Jeffamine ED2001, 5mM MgCl2, 8mM BaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 125.54 α = 90
b = 78.48 β = 103.17
c = 142.99 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r mirrors 2013-07-27
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRF BEAMLINE BL17U 0.9792 SSRF BL17U

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
2.6 40 98.7 -- -- -- -- 41994 41448 1.0 1.0 --
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)
2.595 2.69 95.0 -- -- -- -- --

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 2.595 34.184 -- 1.34 42559 41437 2098 98.35 -- 0.242 0.2399 0.2828 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 2.5948 2.6552 -- 131 2328 0.3797 0.3968 -- 88.0
X Ray Diffraction 2.6552 2.7215 -- 135 2659 0.3752 0.4668 -- 99.0
X Ray Diffraction 2.7215 2.7951 -- 153 2594 0.3522 0.347 -- 99.0
X Ray Diffraction 2.7951 2.8773 -- 156 2595 0.3313 0.422 -- 99.0
X Ray Diffraction 2.8773 2.9701 -- 132 2668 0.3181 0.3585 -- 99.0
X Ray Diffraction 2.9701 3.0762 -- 138 2648 0.3034 0.3982 -- 99.0
X Ray Diffraction 3.0762 3.1993 -- 157 2590 0.2978 0.3124 -- 99.0
X Ray Diffraction 3.1993 3.3448 -- 115 2655 0.2656 0.3256 -- 99.0
X Ray Diffraction 3.3448 3.5209 -- 144 2665 0.2477 0.2944 -- 99.0
X Ray Diffraction 3.5209 3.7413 -- 145 2621 0.2408 0.2973 -- 99.0
X Ray Diffraction 3.7413 4.0297 -- 170 2628 0.2312 0.2812 -- 99.0
X Ray Diffraction 4.0297 4.4345 -- 118 2665 0.1991 0.2524 -- 99.0
X Ray Diffraction 4.4345 5.0744 -- 130 2675 0.1631 0.1833 -- 99.0
X Ray Diffraction 5.0744 6.3864 -- 139 2689 0.2415 0.2742 -- 99.0
X Ray Diffraction 6.3864 34.1874 -- 135 2659 0.2314 0.2546 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 13.304
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -4.7817
Anisotropic B[2][2] -2.4816
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.6292
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.009
f_chiral_restr 0.088
f_dihedral_angle_d 20.341
f_angle_d 1.465
f_bond_d 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8179
Nucleic Acid Atoms 186
Heterogen Atoms 0
Solvent Atoms 90

Software

Computing
Computing Package Purpose
CBASS Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.3_928) refinement
PHASER model building
CBASS data collection