X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.6
Temperature 293.0
Details 2 ul protein solution (5 mg/ml protein in 20 mM Tris, pH 7.6, 150 mM NaCl, 10 mM DTT) were mixed with 2 ul reservoir buffer consisting of 100 mM Hepes, pH 7.6, 10 mM DTT, and 14-21% (w/v) polyethylene glycol (PEG) 4000 above 500 ul reservoir buffer. Colorless plate-shaped crystals were obtained within a few days. VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 68.91 α = 90
b = 69.36 β = 90.11
c = 84.18 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2004-04-24
Diffraction Radiation
Monochromator Protocol
Double-crystal, Si(111) liquid N2 cooled SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 5.0.2 -- ALS 5.0.2

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
2.05 50 99.1 0.162 -- -- 3.8 -- 49562 -- 2.0 --
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)
2.05 2.12 98.4 0.535 -- 6.7 3.7 4839

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 2.05 50.0 2.0 -- 49982 49521 4614 99.1 -- -- 0.209 0.246 --
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 2.05 2.06 851 79 -- 0.239 0.297 -- 1.7
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 29.411
Anisotropic B[1][1] 10.411
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.293
Anisotropic B[2][2] -16.469
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 6.058
RMS Deviations
Key Refinement Restraint Deviation
c_scbond_it 2.221
c_bond_d 0.006
c_scangle_it 3.312
c_mcangle_it 2.483
c_mcbond_it 1.514
c_angle_d 1.268
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6096
Nucleic Acid Atoms 0
Heterogen Atoms 4
Solvent Atoms 389

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
MOLREP phasing
CNS refinement
PDB_EXTRACT data extraction version: 2.000
HKL-2000 data collection
HKL-2000 data reduction
PHASER phasing