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 ADSC QUANTUM 315r -- 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_chiral_restr 0.077
f_bond_d 0.014
f_dihedral_angle_d 15.952
f_angle_d 1.407
f_plane_restr 0.007
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

Software
Software Name Purpose
PHENIX refinement version: (PHENIX.REFINE)
XDS data reduction
XDS data scaling
BALBES phasing