X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Small Tubes
pH 4.6
Temperature 293.0
Details PURE PROTEIN EXTENSIVELY DIALYSED AGAINST SODIUM ACETATE BUFFER AT PH 4.6 WAS USED IN THE CRYSTALLIZATION TRIALS. CRYSTALS WERE OBTAINED BY THE BATCH METHOD USING 4-5 MG/ML PROTEIN IN 0.05 M SODIUM ACETATE BUFFER CONTAINING 0.2 M SODIUM CHLORIDE, 1.5 MM LACTOSE AND 0.05 %SODIUM AZIDE. THE PRECIPITANT USED WAS PEG 8000, A SOLUTION OF WHICH IN THE SAME BUFFER WAS ADDED TO A FINAL CONCENTRATION OF ABOUT 12%. THE TUBES WERE LEFT UNDISTURBED FOR ABOUT TWO WEEKS, BY WHICH TIME CRYSTALS SUITABLE FOR DATA COLLECTION GREW., SMALL TUBES, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 128.32 α = 90
b = 126.82 β = 116.14
c = 85.61 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 293
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH MIRRORS --
Diffraction Radiation
Monochromator Protocol
-- 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
2.6 20 86.3 0.134 -- -- 4.75 -- 65505 -- -- 12.3

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 2.6 10.0 -- 0.0 -- 58584 1168 78.9 -- 0.212 0.207 0.272 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 2.6 2.76 -- 175 7337 0.289 0.363 0.027 60.8
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model GROUP
Mean Isotropic B 21.9
RMS Deviations
Key Refinement Restraint Deviation
x_mcangle_it 10.52
x_bond_d 0.01
x_scbond_it 4.06
x_scangle_it 5.72
x_improper_angle_d 1.39
x_angle_deg 1.7
x_mcbond_it 6.67
x_dihedral_angle_d 27.6
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.3
Luzzati Sigma A (Observed) 0.4
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.41
Luzzati Sigma A (R-Free Set) 0.51
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 13944
Nucleic Acid Atoms 0
Heterogen Atoms 85
Solvent Atoms 703

Software

Software
Software Name Purpose
AMoRE phasing
X-PLOR refinement version: 3.851
MARXDS data reduction
DENZO data reduction
SCALEPACK data scaling