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, MICRODIALYSIS, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 120.68 α = 90
b = 120.68 β = 90
c = 142.52 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 -- 2012-01-18
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
2.1 50 100.0 0.107 -- -- 23.1 70569 70569 -- -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)
2.0976 2.18 100.0 0.562 -- -- 21.1 6979

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
-- 2.0976 49.062 -- 0.0 -- 70565 3564 99.84 -- 0.1771 0.1751 0.2152 --
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 2.0976 2.1263 -- 135 2550 0.2158 0.2451 -- 96.0
X Ray Diffraction 2.1263 2.1567 -- 146 2648 0.2129 0.2907 -- 100.0
X Ray Diffraction 2.1567 2.1889 -- 157 2622 0.2053 0.2756 -- 100.0
X Ray Diffraction 2.1889 2.2231 -- 152 2684 0.1949 0.2499 -- 100.0
X Ray Diffraction 2.2231 2.2595 -- 132 2630 0.1945 0.2354 -- 100.0
X Ray Diffraction 2.2595 2.2985 -- 144 2667 0.1933 0.2592 -- 100.0
X Ray Diffraction 2.2985 2.3403 -- 132 2657 0.1977 0.2447 -- 100.0
X Ray Diffraction 2.3403 2.3853 -- 138 2643 0.1919 0.2394 -- 100.0
X Ray Diffraction 2.3853 2.434 -- 143 2681 0.189 0.2376 -- 100.0
X Ray Diffraction 2.434 2.4869 -- 150 2635 0.1881 0.2552 -- 100.0
X Ray Diffraction 2.4869 2.5447 -- 133 2685 0.1785 0.2473 -- 100.0
X Ray Diffraction 2.5447 2.6084 -- 134 2668 0.1882 0.2087 -- 100.0
X Ray Diffraction 2.6084 2.6789 -- 145 2672 0.1865 0.2499 -- 100.0
X Ray Diffraction 2.6789 2.7577 -- 134 2683 0.1879 0.2394 -- 100.0
X Ray Diffraction 2.7577 2.8467 -- 148 2653 0.195 0.2572 -- 100.0
X Ray Diffraction 2.8467 2.9485 -- 140 2702 0.1974 0.2693 -- 100.0
X Ray Diffraction 2.9485 3.0665 -- 159 2654 0.1885 0.2488 -- 100.0
X Ray Diffraction 3.0665 3.206 -- 141 2662 0.1914 0.2313 -- 100.0
X Ray Diffraction 3.206 3.375 -- 141 2708 0.1867 0.2395 -- 100.0
X Ray Diffraction 3.375 3.5864 -- 153 2679 0.1759 0.2049 -- 100.0
X Ray Diffraction 3.5864 3.8632 -- 130 2715 0.1699 0.2114 -- 100.0
X Ray Diffraction 3.8632 4.2518 -- 139 2717 0.1478 0.195 -- 100.0
X Ray Diffraction 4.2518 4.8666 -- 167 2720 0.1417 0.1716 -- 100.0
X Ray Diffraction 4.8666 6.1295 -- 135 2764 0.1668 0.1911 -- 100.0
X Ray Diffraction 6.1295 49.0756 -- 136 2902 0.1674 0.1671 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 56.7152
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 15.069
f_plane_restr 0.005
f_chiral_restr 0.076
f_angle_d 1.122
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7082
Nucleic Acid Atoms 0
Heterogen Atoms 63
Solvent Atoms 496

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL 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