X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7
Details PROTEIN BOUND TO GPPNHP WAS CRYSTALLIZED IN 1.8-2.0M (NH4)2SO3, 100MM SODIUM ACETATE, H 6.0, 1MM MGSO4, 1MM GPPNHP, AND 5MM DTT. PRIOR TO DATA COLLECTION CRYSTALS WERE TRANSFERED TO 2.0M LI2SO4, 1MM GPPNHP, 3MM DTT, 1MM MGSO4, 100MM BES, PH 7.0, AND 15% GLYCEROL. CRYSTALS WERE FLASH FROZEN IN LIQUID PROPANE.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 80.05 α = 90
b = 80.05 β = 90
c = 105.55 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 1998-06
CCD ADSC QUANTUM 4 -- 1998-06
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CHESS BEAMLINE F1 -- CHESS F1
SYNCHROTRON CHESS BEAMLINE A1 -- CHESS A1

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
1.5 15 90.2 0.051 -- -- 3.92 57771 57771 -- 0.0 15.94
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)
1.5 1.55 77.4 0.14 -- 7.5 2.5 --

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 1.5 15.0 -- 1.0 -- 57291 2895 90.84 -- -- 0.213 0.235 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 1.5 1.57 -- 324 6172 0.246 0.242 -- 83.1
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 18.02
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 4.17
x_scbond_it 2.619
x_mcangle_it 2.166
x_mcbond_it 1.368
x_improper_angle_d 1.36
x_bond_d 0.011
x_angle_deg 1.37
x_dihedral_angle_d 22.83
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2543
Nucleic Acid Atoms 0
Heterogen Atoms 33
Solvent Atoms 157

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