X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 291.0
Details Co-crystallization trial with mouse Nogo54, an extracellular construct derived from the NgR ligand Nogo-A (UNIPROT Q99P72, residues 1025-1078). Nogo54 was purified in 150 mM NaCl, 20 mM HEPES pH 7.0 at a concentration of 3.3 mg/mL and mixed in a 1:1 molar ratio with Endo-Hf-deglycosylated NgRa at a concentration of 10 mg/mL. Crystals were grown in a condition of 0.2 M ammonium sulfate, 0.1 M Bis-Tris pH 6.5, 25% (w/v) PEG3350.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 90.63 α = 90
b = 90.63 β = 90
c = 45.62 γ = 90
Symmetry
Space Group P 41

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M-F -- 2014-04-27
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-1 1.0 ESRF ID23-1

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
2.5 90.63 100.0 -- 0.066 -- 7.4 -- 13084 -- -- --
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)
2.5 2.61 100.0 -- 0.912 2.4 7.6 --

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 2.5 90.63 -- 1.35 -- 13057 650 99.86 -- 0.2201 0.2186 0.2479 --
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 2.5002 2.6932 -- 135 2450 0.3051 0.3442 -- 100.0
X Ray Diffraction 2.6932 2.9643 -- 128 2456 0.3122 0.3991 -- 100.0
X Ray Diffraction 2.9643 3.3933 -- 124 2465 0.3047 0.4354 -- 100.0
X Ray Diffraction 3.3933 4.2752 -- 120 2495 0.221 0.2429 -- 100.0
X Ray Diffraction 4.2752 90.6896 -- 143 2541 0.1787 0.1894 -- 100.0
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.123
f_chiral_restr 0.052
f_bond_d 0.004
f_plane_restr 0.003
f_dihedral_angle_d 19.4
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2419
Nucleic Acid Atoms 0
Heterogen Atoms 152
Solvent Atoms 6

Software

Software
Software Name Purpose
PHENIX refinement version: (1.11.1_2575: ???)
iMOSFLM data reduction
Aimless data scaling
PHASER phasing