X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.2
Temperature 293.0
Details 0.1 M Tris-HCl, pH 8.2, 0.3 M calcium acetate, 12%-14% PEG8000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 49.6 α = 90
b = 170 β = 97
c = 51.1 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
PIXEL DECTRIS PILATUS 6M -- 2013-11-21
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X25 1.100 NSLS X25

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
2.9 50 96.8 0.094 -- -- 2.1 18578 17984 2.0 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)
2.9 3.0 88.4 0.415 -- 1.7 1.9 --

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 2.9 37.696 -- 1.38 18578 17984 872 96.78 -- 0.1976 0.1948 0.2509 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 2.9 3.0816 -- 143 2572 0.2907 0.373 -- 88.0
X Ray Diffraction 3.0816 3.3194 -- 143 2901 0.2495 0.3599 -- 98.0
X Ray Diffraction 3.3194 3.6532 -- 172 2867 0.2064 0.3126 -- 99.0
X Ray Diffraction 3.6532 4.1813 -- 134 2941 0.1802 0.2302 -- 99.0
X Ray Diffraction 4.1813 5.2657 -- 135 2907 0.1737 0.2096 -- 99.0
X Ray Diffraction 5.2657 37.6994 -- 145 2924 0.1707 0.1941 -- 98.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.007
f_chiral_restr 0.055
f_dihedral_angle_d 15.666
f_angle_d 1.374
f_bond_d 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4697
Nucleic Acid Atoms 678
Heterogen Atoms 2
Solvent Atoms 8

Software

Computing
Computing Package Purpose
CBASS Data Collection
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
COMO Structure Solution
PHENIX (phenix.refine: 1.8.4_1496) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8.4_1496) refinement
COMO model building
CBASS data collection