X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
pH 7
Details STOCK: 60 MG BOVINE TRYPSIN (SIGMA) PLUS 5 MG BENZAMIDINE (SIGMA) IN 1 ML OF HEPES BUFFER 0.1M PH 7.0 AND 3 MM CACL2. COCKTAIL: 15% PEG 3350 IN 0.1 M HEPES PH 7.0 ALSO CONTAINING 10 MG/ML SALMON SPERM PROTAMINE (SIGMA) DROP: 2 UL STOCK PLUS 2 UL COCKTAIL IN CRYSCHEM PLATES AT 22 DEG C.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 53.92 α = 90
b = 56.69 β = 90
c = 66.05 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 125
Diffraction Detector
Detector Diffraction Type Details Collection Date
PROTEUM X8 BRUKER AXS MIRROR 2006-08-03
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE BRUKER MICROSTAR -- -- --

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
1.5 25.09 99.3 0.05 -- -- 7.46 -- 31641 -- 2.0 --
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)
1.5 1.57 95.9 0.31 -- 3.84 3.32 --

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 1.5 25.09 -- -- -- 31363 1664 99.8 -- 0.155 0.154 0.176 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 1.5 1.54 -- 130 2245 0.199 0.281 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 12.45
Anisotropic B[1][1] -0.1
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.08
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.03
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.886
r_scbond_it 3.451
r_mcangle_it 2.691
r_mcbond_it 1.739
r_nbd_refined 0.191
r_gen_planes_other 0.001
r_gen_planes_refined 0.006
r_chiral_restr 0.086
r_dihedral_angle_4_deg 15.038
r_dihedral_angle_3_deg 11.833
r_dihedral_angle_2_deg 40.002
r_dihedral_angle_1_deg 6.466
r_angle_other_deg 0.892
r_angle_refined_deg 1.324
r_bond_other_d 0.001
r_bond_refined_d 0.01
r_nbd_other 0.193
r_nbtor_refined 0.174
r_nbtor_other 0.086
r_xyhbond_nbd_refined 0.139
r_symmetry_vdw_refined 0.165
r_symmetry_vdw_other 0.247
r_symmetry_hbond_refined 0.149
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1708
Nucleic Acid Atoms 0
Heterogen Atoms 18
Solvent Atoms 208

Software

Computing
Computing Package Purpose
BRUKER Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
EPMR, SHAKEANDWARP Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0019 refinement
SHAKEANDWARP model building
EPMR model building