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_scangle_it 4.603
p_scbond_it 3.366
p_bond_d 0.011
p_angle_d 0.026
p_planar_d 0.03
p_chiral_restr 0.12
p_singtor_nbd 0.174
p_multtor_nbd 0.19
p_xyhbond_nbd 0.125
p_planar_tor 3.9
p_staggered_tor 13.4
p_transverse_tor 25.9
p_mcbond_it 0.941
p_mcangle_it 1.364
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

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
CCP4 (TRUNCATE) Data Reduction (data scaling)
MLPHARE Structure Solution
REFMAC 4.0.6 Structure Refinement
Software
Software Name Purpose
REFMAC version: 4.0.6 refinement
MLPHARE model building
TRUNCATE data reduction
DENZO data collection