X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Microdialysis
pH 5.7
Temperature 298.0
Details 40 mM sodium citrate, 1 mM 2-mercaptoethanol, 0.2 mM EDTA, 1.0 mM dCTP, pH 5.7 (crystals soaked in 5 mM UTP and 5 mM Mg2+), MICRODIALYSIS, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 121.21 α = 90
b = 121.21 β = 90
c = 141.76 γ = 120
Symmetry
Space Group P 3 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2012-01-19
Diffraction Radiation
Monochromator Protocol
Rosenbaum-Rock double crystal sagittal focusing monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X29A 1.075 NSLS X29A

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
2.09 50 100.0 0.145 -- -- 22.3 71745 71745 -- -3.0 --
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)
2.0889 2.18 100.0 0.684 -- -- 20.3 7107

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 2.0889 49.22 -- 0.0 71777 71741 3630 99.95 -- 0.1676 0.1652 0.2125 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 2.0889 2.1164 -- 130 2560 0.1975 0.254 -- 99.0
X Ray Diffraction 2.1164 2.1454 -- 142 2603 0.1935 0.233 -- 100.0
X Ray Diffraction 2.1454 2.176 -- 126 2569 0.1874 0.2465 -- 100.0
X Ray Diffraction 2.176 2.2085 -- 161 2590 0.1772 0.2467 -- 100.0
X Ray Diffraction 2.2085 2.243 -- 140 2610 0.1761 0.2386 -- 100.0
X Ray Diffraction 2.243 2.2798 -- 133 2571 0.1782 0.2515 -- 100.0
X Ray Diffraction 2.2798 2.3191 -- 139 2607 0.1773 0.2325 -- 100.0
X Ray Diffraction 2.3191 2.3613 -- 151 2579 0.1738 0.2622 -- 100.0
X Ray Diffraction 2.3613 2.4067 -- 132 2588 0.1706 0.2293 -- 100.0
X Ray Diffraction 2.4067 2.4558 -- 132 2606 0.1645 0.2495 -- 100.0
X Ray Diffraction 2.4558 2.5092 -- 137 2608 0.1594 0.2037 -- 100.0
X Ray Diffraction 2.5092 2.5676 -- 150 2581 0.1639 0.221 -- 100.0
X Ray Diffraction 2.5676 2.6318 -- 153 2616 0.1696 0.2647 -- 100.0
X Ray Diffraction 2.6318 2.703 -- 135 2615 0.179 0.249 -- 100.0
X Ray Diffraction 2.703 2.7825 -- 154 2590 0.1772 0.2303 -- 100.0
X Ray Diffraction 2.7825 2.8723 -- 143 2594 0.1809 0.2392 -- 100.0
X Ray Diffraction 2.8723 2.9749 -- 131 2618 0.1737 0.2561 -- 100.0
X Ray Diffraction 2.9749 3.094 -- 166 2583 0.1786 0.2041 -- 100.0
X Ray Diffraction 3.094 3.2348 -- 130 2633 0.1778 0.2223 -- 100.0
X Ray Diffraction 3.2348 3.4053 -- 142 2624 0.1668 0.2152 -- 100.0
X Ray Diffraction 3.4053 3.6186 -- 117 2666 0.1609 0.1848 -- 100.0
X Ray Diffraction 3.6186 3.8979 -- 133 2656 0.1538 0.2063 -- 100.0
X Ray Diffraction 3.8979 4.29 -- 143 2635 0.1374 0.1803 -- 100.0
X Ray Diffraction 4.29 4.9102 -- 136 2674 0.1311 0.1721 -- 100.0
X Ray Diffraction 4.9102 6.1845 -- 133 2715 0.1677 0.2026 -- 100.0
X Ray Diffraction 6.1845 49.2341 -- 141 2820 0.1755 0.1831 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 39.2654
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 14.029
f_plane_restr 0.005
f_chiral_restr 0.077
f_angle_d 1.07
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7149
Nucleic Acid Atoms 0
Heterogen Atoms 118
Solvent Atoms 634

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
HKL data reduction