X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 290.0
Details MCSG1 C12: 0.1 M Bis-Tris: HCl, pH 6.5 25 % (w/v) PEG 3350 cryo:15% Ethylene Glycol. PW37974 22.5mg/mL, 0.4+0.4 puck xbp1-2

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 118.64 α = 90
b = 118.64 β = 90
c = 98.98 γ = 120
Symmetry
Space Group P 63

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-300 Beryllium Lenses 2017-03-15
Diffraction Radiation
Monochromator Protocol
Diamond [111] SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-F 0.97856 APS 21-ID-F

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 34.25 100.0 0.054 -- -- 8.912 -- 53461 -- -3.0 30.44
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)
2.0 2.05 100.0 0.533 -- 4.12 8.919 --

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 2.0 34.248 -- 1.35 -- 53440 2050 99.96 -- 0.1436 0.1423 0.1765 --
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 2.0 2.0465 -- 139 3398 0.1821 0.2195 0.0 100.0
X Ray Diffraction 2.0465 2.0977 -- 129 3445 0.1716 0.2005 0.0 100.0
X Ray Diffraction 2.0977 2.1544 -- 129 3406 0.1683 0.2249 0.0 100.0
X Ray Diffraction 2.1544 2.2178 -- 139 3396 0.1556 0.2253 0.0 100.0
X Ray Diffraction 2.2178 2.2893 -- 140 3408 0.159 0.193 0.0 100.0
X Ray Diffraction 2.2893 2.3711 -- 139 3438 0.1503 0.1943 0.0 100.0
X Ray Diffraction 2.3711 2.466 -- 125 3415 0.1464 0.1919 0.0 100.0
X Ray Diffraction 2.466 2.5782 -- 154 3411 0.1481 0.1857 0.0 100.0
X Ray Diffraction 2.5782 2.7141 -- 127 3438 0.1612 0.2141 0.0 100.0
X Ray Diffraction 2.7141 2.8841 -- 126 3427 0.1506 0.1923 0.0 100.0
X Ray Diffraction 2.8841 3.1066 -- 147 3406 0.1592 0.194 0.0 100.0
X Ray Diffraction 3.1066 3.419 -- 160 3401 0.1438 0.1497 0.0 100.0
X Ray Diffraction 3.419 3.9131 -- 142 3440 0.1343 0.1723 0.0 100.0
X Ray Diffraction 3.9131 4.9278 -- 132 3457 0.1112 0.1465 0.0 100.0
X Ray Diffraction 4.9278 34.2534 -- 122 3504 0.138 0.159 0.0 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 39.7166
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 10.969
f_bond_d 0.006
f_chiral_restr 0.064
f_plane_restr 0.005
f_angle_d 0.879
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4996
Nucleic Acid Atoms 0
Heterogen Atoms 74
Solvent Atoms 498

Software

Software
Software Name Purpose
XSCALE data scaling
PHENIX refinement version: dev_2733
PDB_EXTRACT data extraction version: 3.22
MoRDa phasing
XDS data reduction