X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 5
Temperature 293.0
Details 100 mM Bicine pH 9, 1.6 M (NH4)3PO4, 5 mM TCEP and 0.2 mM PLP, VAPOR DIFFUSION, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 160.05 α = 90
b = 160.05 β = 90
c = 159.83 γ = 120
Symmetry
Space Group P 3 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r multilayer mirror 2011-04-01
Diffraction Radiation
Monochromator Protocol
Diamond (111), Ge(220) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-1 0.9334 ESRF ID14-1

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
1.9 99 99.9 0.068 -- -- 5.4 185699 185454 0.0 0.0 --
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)
1.899 1.97 99.1 0.371 -- 4.3 4.4 --

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 1.899 49.783 -- 1.34 185699 185406 9313 99.89 -- 0.1562 0.1546 0.1856 --
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 1.899 1.9206 -- 297 5701 0.1974 0.2241 -- 98.0
X Ray Diffraction 1.9206 1.9432 -- 293 5888 0.1856 0.2443 -- 100.0
X Ray Diffraction 1.9432 1.9669 -- 313 5812 0.1705 0.2087 -- 100.0
X Ray Diffraction 1.9669 1.9918 -- 307 5791 0.1599 0.1845 -- 100.0
X Ray Diffraction 1.9918 2.018 -- 312 5869 0.1573 0.1935 -- 100.0
X Ray Diffraction 2.018 2.0456 -- 310 5806 0.1629 0.2084 -- 100.0
X Ray Diffraction 2.0456 2.0749 -- 285 5872 0.159 0.2089 -- 100.0
X Ray Diffraction 2.0749 2.1058 -- 318 5859 0.1536 0.1883 -- 100.0
X Ray Diffraction 2.1058 2.1387 -- 292 5795 0.1464 0.182 -- 100.0
X Ray Diffraction 2.1387 2.1738 -- 286 5838 0.1476 0.1841 -- 100.0
X Ray Diffraction 2.1738 2.2113 -- 316 5826 0.1492 0.1888 -- 100.0
X Ray Diffraction 2.2113 2.2515 -- 319 5895 0.1491 0.1856 -- 100.0
X Ray Diffraction 2.2515 2.2948 -- 294 5792 0.1514 0.2006 -- 100.0
X Ray Diffraction 2.2948 2.3416 -- 313 5832 0.147 0.1677 -- 100.0
X Ray Diffraction 2.3416 2.3925 -- 316 5879 0.1558 0.2 -- 100.0
X Ray Diffraction 2.3925 2.4482 -- 318 5833 0.1543 0.2027 -- 100.0
X Ray Diffraction 2.4482 2.5094 -- 305 5859 0.1609 0.1828 -- 100.0
X Ray Diffraction 2.5094 2.5773 -- 330 5855 0.1624 0.2073 -- 100.0
X Ray Diffraction 2.5773 2.6531 -- 346 5801 0.1629 0.1867 -- 100.0
X Ray Diffraction 2.6531 2.7387 -- 309 5850 0.1564 0.1977 -- 100.0
X Ray Diffraction 2.7387 2.8366 -- 311 5904 0.1577 0.2142 -- 100.0
X Ray Diffraction 2.8366 2.9502 -- 350 5842 0.158 0.192 -- 100.0
X Ray Diffraction 2.9502 3.0844 -- 316 5902 0.1674 0.1819 -- 100.0
X Ray Diffraction 3.0844 3.247 -- 293 5870 0.1679 0.2124 -- 100.0
X Ray Diffraction 3.247 3.4504 -- 307 5908 0.1619 0.1846 -- 100.0
X Ray Diffraction 3.4504 3.7167 -- 283 5981 0.1498 0.1798 -- 100.0
X Ray Diffraction 3.7167 4.0906 -- 338 5881 0.1301 0.1458 -- 100.0
X Ray Diffraction 4.0906 4.6821 -- 316 5965 0.1259 0.1546 -- 100.0
X Ray Diffraction 4.6821 5.8975 -- 328 5998 0.149 0.1723 -- 100.0
X Ray Diffraction 5.8975 49.7998 -- 292 6189 0.1733 0.1816 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -1.1334
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.1334
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.2669
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.007
f_chiral_restr 0.073
f_plane_restr 0.005
f_dihedral_angle_d 13.916
f_angle_d 1.076
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 14486
Nucleic Acid Atoms 0
Heterogen Atoms 142
Solvent Atoms 1394

Software

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