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 MARMOSAIC 225 mm CCD -- 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_angle_d 1.304
f_dihedral_angle_d 13.606
f_plane_restr 0.006
f_bond_d 0.01
f_chiral_restr 0.09
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

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