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 = 60.47 α = 90
b = 106.6 β = 96.68
c = 83 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 ADSC QUANTUM 315 -- 2012-11-21
Diffraction Radiation
Monochromator Protocol
Double-crystal, Si(111) liquid N2 cooled SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 5.0.2 -- ALS 5.0.2

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
1.6 50 97.7 -- -- -- -- 138245 135066 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)
1.6 1.66 96.1 -- -- -- -- --

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 1.6 42.285 -- 1.34 -- 135040 6743 97.47 -- 0.157 0.1556 0.1833 5% random
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 1.6 1.6135 -- 205 3844 0.2415 0.2824 -- 88.0
X Ray Diffraction 1.6135 1.6325 -- 211 4243 0.2432 0.2743 -- 96.0
X Ray Diffraction 1.6325 1.6524 -- 225 4156 0.2259 0.2846 -- 96.0
X Ray Diffraction 1.6524 1.6733 -- 224 4221 0.2214 0.251 -- 97.0
X Ray Diffraction 1.6733 1.6954 -- 207 4239 0.2073 0.2477 -- 96.0
X Ray Diffraction 1.6954 1.7186 -- 217 4219 0.1972 0.2365 -- 96.0
X Ray Diffraction 1.7186 1.7431 -- 234 4184 0.1912 0.2423 -- 97.0
X Ray Diffraction 1.7431 1.7692 -- 217 4265 0.183 0.2404 -- 97.0
X Ray Diffraction 1.7692 1.7968 -- 222 4239 0.1776 0.2063 -- 97.0
X Ray Diffraction 1.7968 1.8263 -- 206 4294 0.1702 0.2193 -- 97.0
X Ray Diffraction 1.8263 1.8578 -- 213 4238 0.1681 0.1967 -- 97.0
X Ray Diffraction 1.8578 1.8915 -- 209 4299 0.1669 0.2206 -- 97.0
X Ray Diffraction 1.8915 1.9279 -- 212 4258 0.1635 0.1884 -- 97.0
X Ray Diffraction 1.9279 1.9673 -- 239 4247 0.1592 0.211 -- 97.0
X Ray Diffraction 1.9673 2.0101 -- 210 4315 0.1576 0.1719 -- 98.0
X Ray Diffraction 2.0101 2.0568 -- 217 4259 0.1613 0.2036 -- 98.0
X Ray Diffraction 2.0568 2.1082 -- 220 4296 0.1618 0.1827 -- 98.0
X Ray Diffraction 2.1082 2.1652 -- 240 4304 0.1503 0.1861 -- 98.0
X Ray Diffraction 2.1652 2.229 -- 232 4288 0.146 0.1514 -- 98.0
X Ray Diffraction 2.229 2.3009 -- 242 4292 0.1454 0.1811 -- 98.0
X Ray Diffraction 2.3009 2.3831 -- 234 4307 0.1505 0.1794 -- 98.0
X Ray Diffraction 2.3831 2.4785 -- 230 4300 0.1489 0.1721 -- 98.0
X Ray Diffraction 2.4785 2.5913 -- 214 4339 0.1542 0.1888 -- 99.0
X Ray Diffraction 2.5913 2.7279 -- 222 4361 0.1562 0.1945 -- 99.0
X Ray Diffraction 2.7279 2.8988 -- 234 4332 0.1681 0.1966 -- 99.0
X Ray Diffraction 2.8988 3.1225 -- 228 4369 0.154 0.1926 -- 99.0
X Ray Diffraction 3.1225 3.4366 -- 251 4347 0.1414 0.1644 -- 99.0
X Ray Diffraction 3.4366 3.9336 -- 220 4393 0.1276 0.1538 -- 100.0
X Ray Diffraction 3.9336 4.9547 -- 271 4385 0.1207 0.1356 -- 100.0
X Ray Diffraction 4.9547 42.3002 -- 237 4464 0.1566 0.1669 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 8.7574
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.2569
Anisotropic B[2][2] 7.5498
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.524
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 12.433
f_chiral_restr 0.078
f_bond_d 0.008
f_angle_d 1.184
f_plane_restr 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7557
Nucleic Acid Atoms 0
Heterogen Atoms 126
Solvent Atoms 1165

Software

Software
Software Name Purpose
BOS data collection
PHASER phasing
PHENIX refinement version: (phenix.refine: 1.7.3_928)
DENZO data reduction
SCALEPACK data scaling