X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 298.0
Details 100mM HEPES pH7.5 18% (w/v) PEG1500 trace amounts of trypsin , VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 51.07 α = 90
b = 52.49 β = 90
c = 120.79 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2012-05-21
Diffraction Radiation
Monochromator Protocol
Si 111 channel-cut SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-1 0.9792 ESRF ID23-1

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
2.29 50 99.2 -- 0.137 -- 7.17 27871 n/a 0.0 0.0 39.03
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)
2.29 2.35 83.8 -- 0.838 2.58 6.77 1874

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
SAD 2.293 48.141 -- 0.0 27871 27856 1427 99.18 0.1817 0.1817 0.1792 0.2296 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 2.2933 2.3753 -- 116 2467 0.2226 0.2425 -- 93.0
X Ray Diffraction 2.3753 2.4704 -- 137 2673 0.2261 0.3108 -- 100.0
X Ray Diffraction 2.4704 2.5828 -- 172 2624 0.2123 0.2963 -- 100.0
X Ray Diffraction 2.5828 2.719 -- 177 2662 0.2192 0.2897 -- 100.0
X Ray Diffraction 2.719 2.8893 -- 152 2638 0.2074 0.2581 -- 100.0
X Ray Diffraction 2.8893 3.1124 -- 150 2648 0.1917 0.2383 -- 100.0
X Ray Diffraction 3.1124 3.4255 -- 134 2694 0.1706 0.2035 -- 100.0
X Ray Diffraction 3.4255 3.921 -- 157 2656 0.1477 0.2026 -- 100.0
X Ray Diffraction 3.921 4.9393 -- 132 2668 0.1337 0.182 -- 100.0
X Ray Diffraction 4.9393 48.1516 -- 100 2699 0.1986 0.2299 -- 99.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.077
f_dihedral_angle_d 16.027
f_angle_d 1.173
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2359
Nucleic Acid Atoms 0
Heterogen Atoms 2
Solvent Atoms 110

Software

Computing
Computing Package Purpose
DNA Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
SHARP Structure Solution
PHENIX (phenix.refine: 1.8.1_1168) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8.1_1168) refinement
SHARP model building
DNA data collection