X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.8
Temperature 289.0
Details Peptide was included in protein buffer to a final molar ratio of 2:1 relative to protein. Reservoir solution contained 1.2 M sodium citrate, pH 6.8. Equal amounts (1.5 microliters) of protein (9 mg/mL) and reservoir solution were mixed and equillibrated against 500 microliters of crystallization buffer.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 89.72 α = 90
b = 89.72 β = 90
c = 89.72 γ = 90
Symmetry
Space Group P 41 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2012-12-15
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.9791833 APS 19-ID

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
1.75 40.13 99.48 0.055 -- -- 27.3 -- 13010 -- -- --
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)
1.7469 1.8169 -- -- -- 1.844 26.3 --

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 1.747 40.126 -- 1.48 -- 13010 1301 99.48 -- 0.2012 0.1993 0.2179 random selection
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 1.7469 1.8169 -- 135 1224 0.2883 0.3034 -- 96.0
X Ray Diffraction 1.8169 1.8995 -- 142 1264 0.2496 0.2687 -- 100.0
X Ray Diffraction 1.8995 1.9997 -- 142 1280 0.2341 0.2289 -- 100.0
X Ray Diffraction 1.9997 2.125 -- 141 1274 0.2007 0.2523 -- 100.0
X Ray Diffraction 2.125 2.289 -- 145 1301 0.2044 0.2264 -- 100.0
X Ray Diffraction 2.289 2.5193 -- 143 1286 0.1869 0.2089 -- 100.0
X Ray Diffraction 2.5193 2.8838 -- 146 1315 0.1901 0.1981 -- 100.0
X Ray Diffraction 2.8838 3.6329 -- 149 1336 0.1871 0.1994 -- 100.0
X Ray Diffraction 3.6329 40.1364 -- 158 1429 0.1869 0.2088 -- 99.0
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 0.937
f_chiral_restr 0.05
f_plane_restr 0.003
f_dihedral_angle_d 24.464
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 947
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 102

Software

Software
Software Name Purpose
PHENIX refinement version: (1.10pre_2104: ???)
HKL-2000 data reduction
HKL-2000 data scaling
PHENIX phasing
Coot model building