X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7.5
Temperature 277.0
Details Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl, pH 7.5. Reservoir solution: 5.76M K-ACETATE 0.1M NA3-CITRATE, UNDER OIL BATCH, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 70.66 α = 90
b = 70.66 β = 90
c = 141.12 γ = 90
Symmetry
Space Group I 41 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm -- 2012-04-11
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X4C 0.979 NSLS X4C

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 50 100.0 0.095 -- -- 26.9 -- 31660 -- -3.0 --

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 1.8 40.776 -- 1.34 -- 16694 845 98.23 -- 0.1968 0.1957 0.2175 --
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 1.8002 1.913 -- 130 2429 0.2206 0.2273 -- 92.0
X Ray Diffraction 1.913 2.0607 -- 155 2604 0.1828 0.1993 -- 99.0
X Ray Diffraction 2.0607 2.268 -- 143 2625 0.1788 0.2295 -- 99.0
X Ray Diffraction 2.268 2.5962 -- 136 2644 0.201 0.2285 -- 99.0
X Ray Diffraction 2.5962 3.2707 -- 132 2713 0.2003 0.2302 -- 100.0
X Ray Diffraction 3.2707 40.7868 -- 149 2834 0.196 0.206 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 28.242
Anisotropic B[1][1] 3.661
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 3.661
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -7.323
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.082
f_dihedral_angle_d 14.567
f_angle_d 1.167
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 723
Nucleic Acid Atoms 0
Heterogen Atoms 4
Solvent Atoms 89

Software

Computing
Computing Package Purpose
PHENIX (phenix.refine: dev_1269) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.100 data extraction
phenix refinement