X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
Temperature 293.0
Details grown in Linbro plates in hanging or sitting drop geometry. Drops of equal volume of protein (20 mg/ml) and reservoir solution (1 M NaAc pH 3.0, 9-10 % NaCl, 6 % PEG 6000) were mixed. For the measurements, the crystals were equilibrated in 1 M NaAc pH 3.4, 10 % NaCl, VAPOR DIFFUSION, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 79.29 α = 90
b = 79.29 β = 90
c = 38.12 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 293
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL PSI PILATUS 6M -- 2012-03-25
Diffraction Radiation
Monochromator Protocol
SI111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X10SA 0.9997 SLS X10SA

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
1.9 35.4 92.6 -- -- -- -- 9297 9297 0.0 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)
1.9 2.0 95.1 -- -- -- -- --

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 SYNTHESIS 1.906 35.4 0.0 1.36 9193 9193 466 92.62 -- 0.1678 0.1661 0.2001 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 1.906 2.1823 -- 157 2884 0.1713 0.2049 -- 95.0
X Ray Diffraction 2.1823 2.7493 -- 157 2912 0.1566 0.207 -- 93.0
X Ray Diffraction 2.7493 35.4657 -- 152 2931 0.1691 0.1948 -- 90.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -0.5815
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.5815
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.1631
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.007
f_dihedral_angle_d 13.875
f_plane_restr 0.003
f_angle_d 1.048
f_chiral_restr 0.081
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1001
Nucleic Acid Atoms 0
Heterogen Atoms 2
Solvent Atoms 78

Software

Software
Software Name Purpose
PHENIX model building
PHENIX refinement version: (phenix.refine: 1.7.2_869)
XDS data reduction
XDS data scaling
PHENIX phasing