X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Details TRYPSIN (SIGMA T1426) WAS DISOLVED IN 1 MM HCL (PH 2.0), 10 MM CACL2, PURIFIED ON A SUPERDEX 75 16/60 COLUMN (BUFFER: 25 MM MES PH 5.5, 50 MM NACL AND 10 MM CACL2). CRYSTALS GREW FROM EQUAL VOLUMES OF TRYPSIN (11.5 MG/ML) INCUBATED WITH LYOPHILIZED SOTI-III F14A (1.5MM) AND PRECIPITANT SOLUTION (0.1M BICINE PH 9, 20% (W/V) PEG 6000) IN HANGING DROP CRYSTALLIZATION PLATES AT 19C.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 48.51 α = 90
b = 68.38 β = 93.25
c = 109.79 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD (MX-225) MARRESEARCH -- 2011-09-28
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.1 -- BESSY 14.1

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 20 98.7 0.14 -- -- 3.2 -- 48020 -- 2.0 10.57
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)
2.0 2.1 98.5 0.45 -- 2.9 3.2 --

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 2.0 19.889 -- 1.99 -- 48006 2405 98.82 -- 0.1694 0.1667 0.2202 --
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 2.0 2.0408 -- 139 2659 0.2059 0.2947 -- 98.0
X Ray Diffraction 2.0408 2.0851 -- 146 2646 0.1946 0.2422 -- 99.0
X Ray Diffraction 2.0851 2.1336 -- 136 2651 0.1781 0.2855 -- 99.0
X Ray Diffraction 2.1336 2.1869 -- 136 2671 0.1762 0.2503 -- 99.0
X Ray Diffraction 2.1869 2.2459 -- 145 2632 0.175 0.239 -- 98.0
X Ray Diffraction 2.2459 2.3119 -- 144 2712 0.1777 0.2193 -- 99.0
X Ray Diffraction 2.3119 2.3864 -- 153 2628 0.1657 0.2326 -- 99.0
X Ray Diffraction 2.3864 2.4716 -- 135 2708 0.1722 0.2157 -- 99.0
X Ray Diffraction 2.4716 2.5703 -- 136 2658 0.1673 0.2452 -- 99.0
X Ray Diffraction 2.5703 2.687 -- 138 2696 0.173 0.2519 -- 99.0
X Ray Diffraction 2.687 2.8283 -- 152 2670 0.1775 0.2471 -- 99.0
X Ray Diffraction 2.8283 3.005 -- 127 2698 0.1777 0.2255 -- 99.0
X Ray Diffraction 3.005 3.2361 -- 157 2710 0.1718 0.1928 -- 99.0
X Ray Diffraction 3.2361 3.5601 -- 135 2663 0.1695 0.2157 -- 99.0
X Ray Diffraction 3.5601 4.0714 -- 142 2727 0.1474 0.1834 -- 99.0
X Ray Diffraction 4.0714 5.115 -- 136 2708 0.1275 0.1653 -- 99.0
X Ray Diffraction 5.115 19.8901 -- 148 2764 0.1545 0.1992 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 3.845
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.9015
Anisotropic B[2][2] -1.7329
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.1121
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_chiral_restr 0.06
f_dihedral_angle_d 14.015
f_angle_d 0.862
f_bond_d 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5601
Nucleic Acid Atoms 0
Heterogen Atoms 19
Solvent Atoms 656

Software

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (PHENIX.REFINE) Structure Refinement
Software
Software Name Purpose
PHENIX version: (PHENIX.REFINE) refinement
PHASER model building