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 CTP, pH 5.7 (crystals soaked in 5 mM UTP and 5 mM Mg2+), MICRODIALYSIS, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 121.13 α = 90
b = 121.13 β = 90
c = 141.44 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
1.94 50 100.0 0.137 -- -- 22.0 89121 89121 -- -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)
1.9395 2.01 100.0 0.608 -- -- 19.5 8794

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 1.9395 49.179 -- 0.0 89196 89119 4462 99.98 -- 0.1948 0.1926 0.2365 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 1.9395 1.9615 -- 153 2784 0.2003 0.2355 -- 100.0
X Ray Diffraction 1.9615 1.9846 -- 138 2777 0.1996 0.2702 -- 100.0
X Ray Diffraction 1.9846 2.0088 -- 155 2779 0.2065 0.2672 -- 100.0
X Ray Diffraction 2.0088 2.0342 -- 150 2772 0.2111 0.2624 -- 100.0
X Ray Diffraction 2.0342 2.061 -- 161 2829 0.2017 0.2829 -- 100.0
X Ray Diffraction 2.061 2.0892 -- 154 2770 0.1924 0.2723 -- 100.0
X Ray Diffraction 2.0892 2.1191 -- 144 2812 0.1837 0.2151 -- 100.0
X Ray Diffraction 2.1191 2.1507 -- 140 2799 0.1839 0.2447 -- 100.0
X Ray Diffraction 2.1507 2.1843 -- 150 2780 0.1839 0.2439 -- 100.0
X Ray Diffraction 2.1843 2.2201 -- 161 2768 0.175 0.2341 -- 100.0
X Ray Diffraction 2.2201 2.2584 -- 161 2805 0.1791 0.2533 -- 100.0
X Ray Diffraction 2.2584 2.2995 -- 124 2826 0.178 0.2389 -- 100.0
X Ray Diffraction 2.2995 2.3437 -- 151 2787 0.1835 0.2168 -- 100.0
X Ray Diffraction 2.3437 2.3915 -- 153 2800 0.1837 0.2517 -- 100.0
X Ray Diffraction 2.3915 2.4435 -- 145 2828 0.1812 0.238 -- 100.0
X Ray Diffraction 2.4435 2.5004 -- 132 2815 0.1756 0.2089 -- 100.0
X Ray Diffraction 2.5004 2.5629 -- 157 2804 0.183 0.2379 -- 100.0
X Ray Diffraction 2.5629 2.6322 -- 136 2819 0.188 0.2716 -- 100.0
X Ray Diffraction 2.6322 2.7096 -- 148 2809 0.1837 0.2339 -- 100.0
X Ray Diffraction 2.7096 2.7971 -- 154 2807 0.1898 0.2219 -- 100.0
X Ray Diffraction 2.7971 2.897 -- 146 2827 0.1909 0.2304 -- 100.0
X Ray Diffraction 2.897 3.013 -- 146 2840 0.196 0.2455 -- 100.0
X Ray Diffraction 3.013 3.1501 -- 116 2853 0.2006 0.2683 -- 100.0
X Ray Diffraction 3.1501 3.3162 -- 151 2819 0.2043 0.2469 -- 100.0
X Ray Diffraction 3.3162 3.5239 -- 144 2842 0.2014 0.2366 -- 100.0
X Ray Diffraction 3.5239 3.7959 -- 157 2865 0.1902 0.2399 -- 100.0
X Ray Diffraction 3.7959 4.1777 -- 145 2857 0.1842 0.2401 -- 100.0
X Ray Diffraction 4.1777 4.7818 -- 171 2858 0.1811 0.2392 -- 100.0
X Ray Diffraction 4.7818 6.0228 -- 169 2888 0.1984 0.2116 -- 100.0
X Ray Diffraction 6.0228 49.195 -- 150 3038 0.2134 0.2129 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 41.2092
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 15.002
f_plane_restr 0.005
f_chiral_restr 0.077
f_angle_d 1.139
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7140
Nucleic Acid Atoms 0
Heterogen Atoms 120
Solvent Atoms 574

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