X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Details TRYPSIN (SIGMA T1426) WAS DUSIKVED UB 1MM 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 VOL. OF TRYPSIN (11.5 MG/ML) INCUBATED WITH LYOPHILIZED SOTI-III (2.5 MM) AND PRECIPITANT SOLUTION (0.1 M IMIDAZOLE PH 7.5, 12 % (W/V) PEG 8K) IN HANGING DROP CRYSTALLIZATION PLATES AT 19C.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 49.35 α = 90
b = 66.82 β = 90.17
c = 108.89 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 -- 2010-11-30
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
1.7 15 97.3 0.08 -- -- 3.8 -- 75899 -- 2.0 13.88
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)
1.7 1.8 93.7 0.49 -- 2.85 3.8 --

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 1.702 32.04 -- 1.99 -- 75888 3794 97.72 -- 0.1808 0.1787 0.2209 --
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 1.7022 1.7237 -- 130 2487 0.2136 0.2809 -- 93.0
X Ray Diffraction 1.7237 1.7464 -- 138 2617 0.213 0.2616 -- 97.0
X Ray Diffraction 1.7464 1.7703 -- 140 2664 0.2033 0.2424 -- 97.0
X Ray Diffraction 1.7703 1.7956 -- 139 2637 0.1961 0.2558 -- 97.0
X Ray Diffraction 1.7956 1.8224 -- 139 2643 0.2032 0.2447 -- 97.0
X Ray Diffraction 1.8224 1.8509 -- 142 2682 0.1989 0.263 -- 97.0
X Ray Diffraction 1.8509 1.8812 -- 137 2615 0.193 0.2545 -- 97.0
X Ray Diffraction 1.8812 1.9136 -- 140 2660 0.1798 0.2451 -- 97.0
X Ray Diffraction 1.9136 1.9484 -- 138 2619 0.1877 0.2383 -- 97.0
X Ray Diffraction 1.9484 1.9859 -- 142 2706 0.1744 0.2278 -- 98.0
X Ray Diffraction 1.9859 2.0264 -- 141 2662 0.1778 0.2107 -- 98.0
X Ray Diffraction 2.0264 2.0705 -- 139 2645 0.1805 0.2403 -- 98.0
X Ray Diffraction 2.0705 2.1186 -- 139 2639 0.1824 0.2178 -- 98.0
X Ray Diffraction 2.1186 2.1716 -- 142 2698 0.1765 0.2648 -- 98.0
X Ray Diffraction 2.1716 2.2303 -- 139 2657 0.1768 0.2037 -- 98.0
X Ray Diffraction 2.2303 2.2959 -- 142 2695 0.1726 0.2351 -- 98.0
X Ray Diffraction 2.2959 2.37 -- 141 2683 0.1789 0.2388 -- 98.0
X Ray Diffraction 2.37 2.4547 -- 142 2688 0.1803 0.2141 -- 98.0
X Ray Diffraction 2.4547 2.5529 -- 139 2648 0.1842 0.2228 -- 98.0
X Ray Diffraction 2.5529 2.6691 -- 143 2702 0.1798 0.2363 -- 98.0
X Ray Diffraction 2.6691 2.8097 -- 141 2680 0.1949 0.2667 -- 98.0
X Ray Diffraction 2.8097 2.9856 -- 143 2718 0.1897 0.2348 -- 98.0
X Ray Diffraction 2.9856 3.216 -- 141 2691 0.1748 0.2297 -- 98.0
X Ray Diffraction 3.216 3.5392 -- 144 2722 0.1738 0.1809 -- 99.0
X Ray Diffraction 3.5392 4.0505 -- 142 2709 0.1585 0.1985 -- 98.0
X Ray Diffraction 4.0505 5.0999 -- 144 2740 0.1543 0.1828 -- 99.0
X Ray Diffraction 5.0999 32.0456 -- 147 2787 0.1833 0.1936 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 2.6926
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.6891
Anisotropic B[2][2] 0.6962
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.3888
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_chiral_restr 0.09
f_dihedral_angle_d 13.606
f_angle_d 1.304
f_bond_d 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5600
Nucleic Acid Atoms 0
Heterogen Atoms 89
Solvent Atoms 580

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