X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.1
Temperature 291.0
Details 13.75% PEG8000, 0.01 M magnesium chloride, 0.05 M MES, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 123.21 α = 90
b = 150.18 β = 90
c = 53.92 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 85
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2011-07-23
Diffraction Radiation
Monochromator Protocol
Rosenbaum-Rock high-resolution double-crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97912 APS 19-ID

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
1.48 50 87.6 0.081 -- -- 7.1 -- 145786 0.0 -3.0 --
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)
1.48 1.51 39.8 -- -- -- 1.4 3271

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
SAD 1.994 36.032 -- 1.34 -- 68728 3488 99.51 -- 0.1861 0.184 0.2241 --
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 1.994 2.0217 -- 122 2385 0.2297 0.2906 -- 93.0
X Ray Diffraction 2.0217 2.0506 -- 132 2571 0.216 0.262 -- 100.0
X Ray Diffraction 2.0506 2.0812 -- 135 2588 0.2115 0.276 -- 100.0
X Ray Diffraction 2.0812 2.1137 -- 129 2566 0.2107 0.2811 -- 100.0
X Ray Diffraction 2.1137 2.1484 -- 129 2630 0.2113 0.2497 -- 100.0
X Ray Diffraction 2.1484 2.1854 -- 137 2581 0.2051 0.2604 -- 100.0
X Ray Diffraction 2.1854 2.2251 -- 136 2574 0.2073 0.2958 -- 100.0
X Ray Diffraction 2.2251 2.2679 -- 150 2594 0.2057 0.2631 -- 100.0
X Ray Diffraction 2.2679 2.3142 -- 130 2613 0.2078 0.2601 -- 100.0
X Ray Diffraction 2.3142 2.3645 -- 134 2586 0.2004 0.3225 -- 100.0
X Ray Diffraction 2.3645 2.4195 -- 121 2609 0.1974 0.2501 -- 100.0
X Ray Diffraction 2.4195 2.48 -- 145 2580 0.2018 0.256 -- 100.0
X Ray Diffraction 2.48 2.5471 -- 153 2590 0.2043 0.2717 -- 100.0
X Ray Diffraction 2.5471 2.622 -- 120 2613 0.2067 0.2516 -- 100.0
X Ray Diffraction 2.622 2.7066 -- 173 2592 0.1821 0.2427 -- 100.0
X Ray Diffraction 2.7066 2.8033 -- 136 2603 0.1952 0.2378 -- 100.0
X Ray Diffraction 2.8033 2.9155 -- 142 2585 0.1945 0.2288 -- 100.0
X Ray Diffraction 2.9155 3.0481 -- 135 2632 0.195 0.2595 -- 100.0
X Ray Diffraction 3.0481 3.2087 -- 126 2649 0.189 0.2194 -- 100.0
X Ray Diffraction 3.2087 3.4096 -- 145 2639 0.1845 0.23 -- 100.0
X Ray Diffraction 3.4096 3.6726 -- 148 2616 0.1687 0.2121 -- 100.0
X Ray Diffraction 3.6726 4.0418 -- 145 2643 0.1598 0.1867 -- 100.0
X Ray Diffraction 4.0418 4.6256 -- 173 2660 0.1442 0.1725 -- 100.0
X Ray Diffraction 4.6256 5.8238 -- 135 2716 0.163 0.1815 -- 100.0
X Ray Diffraction 5.8238 36.0378 -- 157 2825 0.1858 0.1906 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 30.673
Anisotropic B[1][1] -6.8795
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 3.4778
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.4016
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 12.546
f_plane_restr 0.004
f_chiral_restr 0.069
f_angle_d 1.045
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6295
Nucleic Acid Atoms 0
Heterogen Atoms 24
Solvent Atoms 812

Software

Computing
Computing Package Purpose
HKL-3000 Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
MLPHARE Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
SCALEPACK data reduction
DENZO data collection