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_angle_d 1.166
f_chiral_restr 0.079
f_bond_d 0.006
f_dihedral_angle_d 17.442
f_plane_restr 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

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHASER phasing
PHENIX refinement version: 1.8.1_1168
PDB_EXTRACT data extraction version: 3.11
DNA data collection
HKL-2000 data reduction
HKL-2000 data scaling
MOLREP phasing