5L5M

Plexin A4 full extracellular region, domains 1 to 7 modeled, data to 8 angstrom, spacegroup P4(3)2(1)2


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8
Temperature 293.5
Details 0.8 M ammonium sulfate, 0.4 M Dimethyl (2-hydroxyethyl) ammonium propane sulfonate (NDSB-211), 100 mM TRIS, pH 8.0

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 271.48 α = 90
b = 271.48 β = 90
c = 251.25 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2011-01-24
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I02 0.9796 Diamond I02

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
8 72.13 99.5 0.13 -- -- 3.7 -- 10298 -- -- --
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)
8.0 -- -- 0.894 -- -- -- --

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 8.0 72.126 -- 0.35 -- 10298 917 99.4 -- 0.3743 0.3732 0.395 --
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 8.0004 8.4216 -- 139 2575 0.4176 0.3746 -- 100.0
X Ray Diffraction 8.4216 8.9483 -- 149 2537 0.4054 0.4919 -- 100.0
X Ray Diffraction 8.9483 9.6377 -- 139 2570 0.3858 0.3818 -- 100.0
X Ray Diffraction 9.6377 10.6049 -- 139 2531 0.3597 0.3873 -- 100.0
X Ray Diffraction 10.6049 12.1331 -- 144 2572 0.3345 0.3442 -- 100.0
X Ray Diffraction 12.1331 15.2626 -- 94 2595 0.3551 0.4245 -- 100.0
X Ray Diffraction 15.2626 72.1287 -- 113 2514 0.3895 0.3984 -- 97.0
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.019
f_chiral_restr 0.132
f_plane_restr 0.019
f_dihedral_angle_d 13.597
f_angle_d 2.473
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7189
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 0

Software

Software
Software Name Purpose
PHENIX refinement version: 1.8.2_1309
iMOSFLM data reduction
Aimless data scaling
PHASER phasing