X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

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
CCD Bruker Platinum 135 MIRROR 2006-08-03
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE BRUKER AXS 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_angle_other_deg 0.892
r_dihedral_angle_4_deg 15.038
r_nbd_other 0.193
r_nbtor_refined 0.174
r_gen_planes_other 0.001
r_gen_planes_refined 0.006
r_nbtor_other 0.086
r_dihedral_angle_1_deg 6.466
r_scbond_it 3.451
r_dihedral_angle_3_deg 11.833
r_mcbond_it 1.739
r_angle_refined_deg 1.324
r_symmetry_vdw_refined 0.165
r_mcangle_it 2.691
r_bond_other_d 0.001
r_bond_refined_d 0.01
r_xyhbond_nbd_refined 0.139
r_nbd_refined 0.191
r_dihedral_angle_2_deg 40.002
r_symmetry_vdw_other 0.247
r_scangle_it 4.886
r_symmetry_hbond_refined 0.149
r_chiral_restr 0.086
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

Software
Software Name Purpose
BRUKER data reduction
SCALEPACK data scaling
EPMR phasing
SHAKEANDWARP phasing
REFMAC refinement version: 5.2.0019