X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.1
Temperature 293.0
Details 1:2 PROTEIN/DNA RATIO, 14% PEG 3350, 0.14M Li-Acetate, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.54 α = 82.96
b = 58.16 β = 87.78
c = 77.97 γ = 73.57
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 TOROIDAL MIRROR 2008-02-25
Diffraction Radiation
Monochromator Protocol
DIAMOND (111), GE(220) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-2 -- ESRF ID14-2

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
1.69 40 94.7 0.047 -- -- 3.9 -- 96978 0.0 0.0 --
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)
1.69 1.72 64.4 0.355 -- -- 3.7 3280

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 1.7 30.118 0.0 1.97 95621 95621 4783 95.33 -- 0.1645 0.1628 0.1971 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 1.7 1.7193 -- 117 2076 0.2205 0.2811 -- 66.0
X Ray Diffraction 1.7193 1.7396 -- 122 2305 0.2057 0.2297 -- 73.0
X Ray Diffraction 1.7396 1.7608 -- 140 2694 0.2014 0.2333 -- 84.0
X Ray Diffraction 1.7608 1.7831 -- 159 2992 0.2035 0.2684 -- 96.0
X Ray Diffraction 1.7831 1.8065 -- 189 3081 0.1873 0.2391 -- 97.0
X Ray Diffraction 1.8065 1.8313 -- 161 3079 0.1888 0.2524 -- 97.0
X Ray Diffraction 1.8313 1.8574 -- 155 3062 0.1827 0.2047 -- 97.0
X Ray Diffraction 1.8574 1.8851 -- 167 3062 0.1827 0.2371 -- 97.0
X Ray Diffraction 1.8851 1.9146 -- 143 3048 0.1833 0.2039 -- 97.0
X Ray Diffraction 1.9146 1.946 -- 177 3171 0.1863 0.2602 -- 97.0
X Ray Diffraction 1.946 1.9795 -- 178 2988 0.181 0.2108 -- 97.0
X Ray Diffraction 1.9795 2.0155 -- 129 3178 0.1791 0.2444 -- 97.0
X Ray Diffraction 2.0155 2.0543 -- 154 3071 0.1705 0.2223 -- 97.0
X Ray Diffraction 2.0543 2.0962 -- 169 3117 0.1705 0.2113 -- 97.0
X Ray Diffraction 2.0962 2.1418 -- 152 3070 0.1707 0.2304 -- 98.0
X Ray Diffraction 2.1418 2.1916 -- 170 3099 0.1678 0.1951 -- 98.0
X Ray Diffraction 2.1916 2.2464 -- 186 3083 0.1602 0.2013 -- 98.0
X Ray Diffraction 2.2464 2.3071 -- 153 3109 0.1652 0.2083 -- 98.0
X Ray Diffraction 2.3071 2.3749 -- 166 3115 0.1687 0.2011 -- 98.0
X Ray Diffraction 2.3749 2.4516 -- 153 3131 0.1723 0.2181 -- 98.0
X Ray Diffraction 2.4516 2.5391 -- 164 3131 0.1713 0.2132 -- 98.0
X Ray Diffraction 2.5391 2.6407 -- 163 3120 0.1735 0.2325 -- 98.0
X Ray Diffraction 2.6407 2.7608 -- 165 3126 0.1759 0.2082 -- 98.0
X Ray Diffraction 2.7608 2.9063 -- 152 3153 0.178 0.2271 -- 99.0
X Ray Diffraction 2.9063 3.0882 -- 157 3137 0.1725 0.2027 -- 99.0
X Ray Diffraction 3.0882 3.3264 -- 195 3095 0.1636 0.1944 -- 99.0
X Ray Diffraction 3.3264 3.6606 -- 160 3166 0.1428 0.1686 -- 99.0
X Ray Diffraction 3.6606 4.1891 -- 159 3152 0.1423 0.1659 -- 99.0
X Ray Diffraction 4.1891 5.2732 -- 170 3140 0.1248 0.1455 -- 99.0
X Ray Diffraction 5.2732 30.1228 -- 158 3087 0.1508 0.1574 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 26.7876
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 17.442
f_plane_restr 0.006
f_chiral_restr 0.079
f_angle_d 1.166
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6119
Nucleic Acid Atoms 934
Heterogen Atoms 76
Solvent Atoms 959

Software

Computing
Computing Package Purpose
DNA Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
MOLREP Structure Solution
PHENIX (phenix.refine: 1.8.1_1168) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Phaser molecular replacement
HKL data reduction