X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7
Details HANGING DROPS CONTAINING 1:1 RATIO OF 20-30 MG/ML PROTEIN SOLUTION AND RESERVOIR SOLUTION (12 % TO 25 % PEG 6,000). THE CRYSTAL WAS SOAKED IN 0.5 M XYLOBIOSE, pH 7.00

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 46.06 α = 90
b = 59.56 β = 110.8
c = 51.13 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 R-AXIS -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE -- -- -- --

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
1.8 30 86.0 0.17 -- -- 6.4 -- 20709 -- 0.0 --
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)
1.8 1.83 37.9 0.338 -- -- 4.3 --

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
FOURIER METHODS 1.8 5.0 -- 0.0 -- 19293 1922 84.3 -- 0.167 0.167 0.212 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 1.8 1.91 -- 164 1543 0.237 0.256 0.02 44.7
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 18.8
Anisotropic B[1][1] 1.266
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.186
Anisotropic B[2][2] -0.115
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.151
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 3.728
x_scbond_it 2.647
x_mcangle_it 2.116
x_mcbond_it 1.494
x_improper_angle_d 0.7
x_bond_d 0.0065
x_angle_deg 1.3
x_dihedral_angle_d 24.0
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.18
Luzzati Sigma A (Observed) 0.16
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.22
Luzzati Sigma A (R-Free Set) 0.13
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2312
Nucleic Acid Atoms 0
Heterogen Atoms 58
Solvent Atoms 131

Software

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