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 MARMOSAIC 225 mm CCD -- 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_dihedral_angle_d 14.015
f_bond_d 0.004
f_chiral_restr 0.06
f_angle_d 0.862
f_plane_restr 0.003
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

Software
Software Name Purpose
PHENIX refinement version: (PHENIX.REFINE)
XDS data reduction
XSCALE data scaling
PHASER phasing