X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.4
Temperature 293.0
Details PROTEIN: 5 MG/ML ALLIINASE, 5 MM HEPES PH 7.4, 10 % (V/V) GLYCEROL, 0.25 MM PYRIDOXAL-5'-PHOSPHATE, 1 MM S-ETHYL-L-CYSTEINE; PRECIPITANT: 2.9 M AMMONIUM SULFATE, 50 MM HEPES PH 7.4 HANGING DROP METHOD(4 MICROL + 4 MICROL), VAPOUR DIFFUSION, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 68.45 α = 90
b = 101.07 β = 90
c = 155.69 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- 2000-04-25
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B 0.8423 EMBL/DESY, Hamburg BW7B

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
1.53 12 98.9 0.055 -- -- 5.8 160747 160747 0.0 -3.0 20.7
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)
1.53 1.56 99.9 0.508 -- 2.1 3.7 8024

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
SIRAS 1.53 12.0 -- 0.0 162892 162892 3264 98.7 -- -- 0.1929 0.2207 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 1.53 1.604 20789 406 -- 0.259 0.281 -- 99.48
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 25.8
RMS Deviations
Key Refinement Restraint Deviation
p_bond_d 0.011
p_multtor_nbd 0.19
p_angle_d 0.026
p_mcbond_it 0.941
p_mcangle_it 1.364
p_planar_d 0.03
p_chiral_restr 0.12
p_planar_tor 3.9
p_xyhbond_nbd 0.125
p_scangle_it 4.603
p_singtor_nbd 0.174
p_transverse_tor 25.9
p_staggered_tor 13.4
p_scbond_it 3.366
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.17
Luzzati Sigma A (Observed) 0.16
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.2
Luzzati Sigma A (R-Free Set) 0.17
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6862
Nucleic Acid Atoms 0
Heterogen Atoms 252
Solvent Atoms 830

Software

Software
Software Name Purpose
DENZO data reduction
TRUNCATE data reduction
MLPHARE phasing
REFMAC refinement version: 4.0.6
CCP4 data scaling version: (TRUNCATE)