3IEK

Crystal Structure of native TTHA0252 from Thermus thermophilus HB8


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.6
Temperature 293.0
Details 50mM sodium citrate, 0.2M ammonium sulfate, 0.6M lithium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 145.22 α = 90
b = 145.7 β = 110.52
c = 119.65 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 95
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2009-02-26
Diffraction Radiation
Monochromator Protocol
transparent diamond double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1 SPring-8 BL26B2

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 99.4 0.057 -- -- 5.7 -- 144351 -- -3.0 --
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 98.7 0.375 -- -- 5.3 14217

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 -- 0.0 -- 137279 13669 94.3 -- -- 0.218 0.25 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 2.05 2.18 21084 2061 -- 0.26 0.292 0.006 87.2
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model restrained
Mean Isotropic B 39.268
Anisotropic B[1][1] 2.897
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 2.702
Anisotropic B[2][2] 0.755
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.652
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 2.905
c_scbond_it 1.957
c_mcbond_it 1.343
c_mcangle_it 2.071
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.26
Luzzati Sigma A (Observed) 0.2
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.3
Luzzati Sigma A (R-Free Set) 0.23
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 13304
Nucleic Acid Atoms 0
Heterogen Atoms 534
Solvent Atoms 597

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
CNS refinement
PDB_EXTRACT data extraction version: 3.005
HKL-2000 data collection
HKL-2000 data reduction
HKL-2000 data scaling
XFIT data reduction