X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.6
Temperature 292.0
Details 0.2uL + 0.2uL drops containing 6mg/mL Nampt, 0.1M Sodium phosphate, 25-29% polyethylene glycol 3350, 0.2M NaCl, 1mM compound, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 60.51 α = 90
b = 106.8 β = 96.59
c = 83.04 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 93
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-300 -- 2012-08-30
Diffraction Radiation
Monochromator Protocol
Double Crystal Monochromator (ACCEL DCM) with an indirectly cryo-cooled first crystal and sagittally focusing second crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-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
1.55 50 100.0 -- -- -- -- 151480 151480 2.0 2.0 --
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)
1.55 1.61 100.0 -- -- -- -- --

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 1.55 46.37 -- 1.35 151480 151425 7612 99.92 -- 0.178 0.1765 0.2069 --
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 1.55 1.5675 -- 279 4676 0.2446 0.2706 -- 99.0
X Ray Diffraction 1.5675 1.5859 -- 235 4774 0.2357 0.2963 -- 100.0
X Ray Diffraction 1.5859 1.6053 -- 254 4771 0.2248 0.2696 -- 100.0
X Ray Diffraction 1.6053 1.6256 -- 250 4765 0.2202 0.267 -- 100.0
X Ray Diffraction 1.6256 1.647 -- 261 4812 0.2102 0.2537 -- 100.0
X Ray Diffraction 1.647 1.6696 -- 242 4788 0.2049 0.253 -- 100.0
X Ray Diffraction 1.6696 1.6934 -- 265 4781 0.2016 0.2421 -- 100.0
X Ray Diffraction 1.6934 1.7187 -- 248 4793 0.1943 0.2436 -- 100.0
X Ray Diffraction 1.7187 1.7455 -- 261 4741 0.1901 0.2224 -- 100.0
X Ray Diffraction 1.7455 1.7742 -- 243 4854 0.1817 0.2192 -- 100.0
X Ray Diffraction 1.7742 1.8048 -- 250 4785 0.1812 0.2252 -- 100.0
X Ray Diffraction 1.8048 1.8376 -- 242 4769 0.176 0.2323 -- 100.0
X Ray Diffraction 1.8376 1.8729 -- 267 4768 0.1785 0.2232 -- 100.0
X Ray Diffraction 1.8729 1.9111 -- 259 4779 0.1775 0.2354 -- 100.0
X Ray Diffraction 1.9111 1.9527 -- 239 4835 0.1715 0.2122 -- 100.0
X Ray Diffraction 1.9527 1.9981 -- 216 4767 0.1679 0.2063 -- 100.0
X Ray Diffraction 1.9981 2.0481 -- 261 4807 0.166 0.1968 -- 100.0
X Ray Diffraction 2.0481 2.1035 -- 235 4830 0.169 0.1989 -- 100.0
X Ray Diffraction 2.1035 2.1654 -- 279 4765 0.1703 0.2106 -- 100.0
X Ray Diffraction 2.1654 2.2353 -- 267 4802 0.1617 0.1845 -- 100.0
X Ray Diffraction 2.2353 2.3152 -- 274 4779 0.1644 0.2005 -- 100.0
X Ray Diffraction 2.3152 2.4078 -- 251 4805 0.171 0.1939 -- 100.0
X Ray Diffraction 2.4078 2.5174 -- 256 4780 0.1666 0.2167 -- 100.0
X Ray Diffraction 2.5174 2.6501 -- 279 4769 0.1704 0.2106 -- 100.0
X Ray Diffraction 2.6501 2.8161 -- 236 4818 0.1758 0.2047 -- 100.0
X Ray Diffraction 2.8161 3.0335 -- 282 4808 0.1796 0.2054 -- 100.0
X Ray Diffraction 3.0335 3.3387 -- 222 4833 0.1743 0.2177 -- 100.0
X Ray Diffraction 3.3387 3.8217 -- 264 4816 0.1695 0.18 -- 100.0
X Ray Diffraction 3.8217 4.8141 -- 240 4855 0.1585 0.1776 -- 100.0
X Ray Diffraction 4.8141 46.3909 -- 255 4888 0.1878 0.1842 -- 100.0
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.106
f_plane_restr 0.009
f_angle_d 1.596
f_dihedral_angle_d 13.739
f_bond_d 0.015
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7519
Nucleic Acid Atoms 0
Heterogen Atoms 146
Solvent Atoms 1006

Software

Software
Software Name Purpose
HKL-2000 data collection
PHASER phasing
PHENIX refinement version: (phenix.refine: 1.8.2_1309)
DENZO data reduction
SCALEPACK data scaling