X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
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 7.0. Equal amounts (1.5 microliters) of protein (8 mg/mL) and reservoir solution were mixed and equillibrated against 500 microliters of crystallization buffer.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 90.23 α = 90
b = 90.23 β = 90
c = 90.23 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 -- 2012-10-18
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97929 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
1.5 28.53 97.95 0.11 -- -- 21.9 -- 20266 -- -- --
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)
1.5003 1.5378 78.0 -- -- -- 14.7 --

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 1.5 28.533 -- 1.48 -- 20266 2024 97.95 -- 0.1754 0.1724 0.2026 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 1.5003 1.5378 -- 112 1010 0.2704 0.2854 -- 78.0
X Ray Diffraction 1.5378 1.5794 -- 137 1230 0.2546 0.2538 -- 95.0
X Ray Diffraction 1.5794 1.6259 -- 139 1275 0.2322 0.2787 -- 99.0
X Ray Diffraction 1.6259 1.6783 -- 144 1292 0.2179 0.2457 -- 100.0
X Ray Diffraction 1.6783 1.7383 -- 144 1303 0.218 0.2546 -- 100.0
X Ray Diffraction 1.7383 1.8079 -- 146 1306 0.1968 0.2452 -- 100.0
X Ray Diffraction 1.8079 1.8902 -- 145 1313 0.1805 0.2234 -- 100.0
X Ray Diffraction 1.8902 1.9898 -- 146 1316 0.1732 0.1966 -- 100.0
X Ray Diffraction 1.9898 2.1144 -- 146 1317 0.1638 0.2211 -- 100.0
X Ray Diffraction 2.1144 2.2776 -- 149 1336 0.1489 0.1931 -- 100.0
X Ray Diffraction 2.2776 2.5067 -- 149 1340 0.1507 0.1876 -- 100.0
X Ray Diffraction 2.5067 2.8691 -- 149 1337 0.1539 0.1914 -- 100.0
X Ray Diffraction 2.8691 3.6136 -- 154 1387 0.1551 0.1708 -- 100.0
X Ray Diffraction 3.6136 28.5384 -- 164 1480 0.1708 0.189 -- 100.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.017
f_dihedral_angle_d 19.935
f_chiral_restr 0.057
f_bond_d 0.011
f_angle_d 1.843
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 965
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 147

Software

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