X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7
Details HEPES 0.1 M PH 8.0, NAH2PO4 0.8 M K2HPO4 0.8 M

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 104.33 α = 90
b = 104.33 β = 90
c = 154.24 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD (QUANTUM 315R) ADSC -- 2008-12-04
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 -- SOLEIL PROXIMA 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
2.01 50 99.9 0.06 -- -- 13.6 -- 57232 -- 2.0 43.8
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)
2.01 2.06 99.5 0.38 -- 5.8 8.7 --

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 2.01 43.209 -- 1.99 -- 57230 2890 99.95 -- 0.2101 0.2085 0.239 --
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 2.0101 2.043 -- 141 2510 0.2794 0.2905 -- 99.0
X Ray Diffraction 2.043 2.0783 -- 126 2554 0.2478 0.2971 -- 100.0
X Ray Diffraction 2.0783 2.1161 -- 118 2573 0.2486 0.3036 -- 100.0
X Ray Diffraction 2.1161 2.1568 -- 123 2537 0.2421 0.2806 -- 100.0
X Ray Diffraction 2.1568 2.2008 -- 136 2566 0.2433 0.3225 -- 100.0
X Ray Diffraction 2.2008 2.2486 -- 136 2549 0.2389 0.2869 -- 100.0
X Ray Diffraction 2.2486 2.3009 -- 119 2561 0.2246 0.2805 -- 100.0
X Ray Diffraction 2.3009 2.3585 -- 114 2589 0.2168 0.3132 -- 100.0
X Ray Diffraction 2.3585 2.4222 -- 132 2572 0.2351 0.2628 -- 100.0
X Ray Diffraction 2.4222 2.4935 -- 149 2556 0.2203 0.2774 -- 100.0
X Ray Diffraction 2.4935 2.574 -- 145 2531 0.222 0.2725 -- 100.0
X Ray Diffraction 2.574 2.666 -- 150 2575 0.2115 0.2612 -- 100.0
X Ray Diffraction 2.666 2.7727 -- 146 2566 0.2169 0.2411 -- 100.0
X Ray Diffraction 2.7727 2.8989 -- 135 2584 0.2098 0.2343 -- 100.0
X Ray Diffraction 2.8989 3.0517 -- 134 2599 0.2191 0.2517 -- 100.0
X Ray Diffraction 3.0517 3.2428 -- 147 2573 0.2087 0.2225 -- 100.0
X Ray Diffraction 3.2428 3.4931 -- 166 2583 0.2091 0.2423 -- 100.0
X Ray Diffraction 3.4931 3.8444 -- 133 2620 0.2038 0.2447 -- 100.0
X Ray Diffraction 3.8444 4.4002 -- 151 2636 0.1734 0.1906 -- 100.0
X Ray Diffraction 4.4002 5.542 -- 149 2669 0.1742 0.2053 -- 100.0
X Ray Diffraction 5.542 43.2185 -- 140 2837 0.2217 0.233 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 46.8
Anisotropic B[1][1] 0.5263
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.5263
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.0526
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.007
f_chiral_restr 0.077
f_dihedral_angle_d 15.952
f_angle_d 1.407
f_bond_d 0.014
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3912
Nucleic Acid Atoms 92
Heterogen Atoms 5
Solvent Atoms 268

Software

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
XDS Data Reduction (data scaling)
BALBES Structure Solution
PHENIX (PHENIX.REFINE) Structure Refinement
Software
Software Name Purpose
PHENIX version: (PHENIX.REFINE) refinement
BALBES model building