X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Micro Dialysis
pH 7.5
Details CPA FROM SIGMA #C0261 WAS DISSOLVED IN 1.0 M LICL WITH 20 MM TRIS-HCL PH 7.5 TO GIVE 12 MG/ML AND USED WITHOUT FURTHER PURIFICATION. THIS PROTEIN SOLUTION WAS PLACED IN 50 MICROL DIALYSIS BUTTONS FROM HAMPTON RESEARCH AND DIALYZED AGAINST A 2 ML RESERVOIR OF THE ABOVE MENTIONED BUFFER WHILE LOWERING THE EXTERNAL LICL CONCENTRATION BY 25% EVERY OTHER DAY. THE CRYSTALS APPEARED A~0.24 M LICL AND WAS STORED AT 0.30M LICL. IF THIS PROCEDURE DOES NOT WORK BY ITSELF AND YOU END UP WITH THE MONOCLINIC ALPHA-FORM (1-307), YOU CAN TRY TO AD TRACES OF TRYPSIN (~10 MICROG/ML) TO THE PROTEIN SOLUTION TO PROVOKE FORMATION OF THE BETA-FORM (3-307), micro dialysis

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 48.79 α = 90
b = 66.85 β = 90
c = 96.02 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 290
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS II -- 1996-12-06
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 -- -- --

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
2 40 94.1 0.038 0.038 -- 4.3 -- 20453 -- -- 19.0
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)
2.0 2.03 67.7 0.157 0.157 7.1 3.9 --

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 2.0 8.0 -- 0.0 -- 20060 977 93.4 -- 0.167 0.167 0.226 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 2.0 2.09 -- 83 1878 0.224 0.252 -- 73.9
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 15.8
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 2.8
x_scbond_it 2.876
x_mcangle_it 2.277
x_mcbond_it 2.221
x_improper_angle_d 1.238
x_bond_d 0.01
x_angle_deg 2.001
x_dihedral_angle_d 22.4
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.2
Luzzati Sigma A (Observed) 0.18
Luzzati Resolution Cutoff (Low) 4.08
Luzzati ESD (R-Free Set) 0.25
Luzzati Sigma A (R-Free Set) 0.18
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2421
Nucleic Acid Atoms 0
Heterogen Atoms 3
Solvent Atoms 277

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
X-PLOR 3.851 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 3.851 refinement
AMORE model building
SCALEPACK data reduction
DENZO data collection