X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 300.0
Details 40-100 mM Sodium Cacodylate, 10-20 % isopropanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 70.38 α = 90
b = 72.76 β = 90
c = 128.88 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 crystal monochrometer 2009-04-10
Diffraction Radiation
Monochromator Protocol
24id-c SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 0.97933 APS 24-ID-C

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
1.65 100 99.6 0.069 -- -- 12.9 -- 79543 -- -- --
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)
1.65 1.68 94.8 0.481 -- -- 4.2 --

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 1.652 31.681 -- 1.34 -- 79450 3982 99.38 -- 0.1534 0.1519 0.1815 --
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 1.652 1.6724 -- 116 2397 0.1955 0.2247 -- 89.0
X Ray Diffraction 1.6724 1.6936 -- 99 2593 0.1911 0.2238 -- 96.0
X Ray Diffraction 1.6936 1.7159 -- 132 2655 0.182 0.2162 -- 98.0
X Ray Diffraction 1.7159 1.7394 -- 162 2645 0.1686 0.209 -- 99.0
X Ray Diffraction 1.7394 1.7642 -- 120 2687 0.1673 0.1787 -- 100.0
X Ray Diffraction 1.7642 1.7906 -- 152 2670 0.1498 0.1922 -- 100.0
X Ray Diffraction 1.7906 1.8185 -- 167 2671 0.1451 0.1943 -- 100.0
X Ray Diffraction 1.8185 1.8483 -- 137 2664 0.1454 0.1504 -- 100.0
X Ray Diffraction 1.8483 1.8802 -- 121 2718 0.1421 0.1916 -- 100.0
X Ray Diffraction 1.8802 1.9144 -- 150 2672 0.1471 0.1842 -- 100.0
X Ray Diffraction 1.9144 1.9512 -- 164 2681 0.1453 0.1839 -- 100.0
X Ray Diffraction 1.9512 1.991 -- 144 2667 0.146 0.1942 -- 100.0
X Ray Diffraction 1.991 2.0343 -- 154 2677 0.1458 0.1765 -- 100.0
X Ray Diffraction 2.0343 2.0816 -- 138 2711 0.1389 0.2112 -- 100.0
X Ray Diffraction 2.0816 2.1337 -- 160 2668 0.1348 0.1615 -- 100.0
X Ray Diffraction 2.1337 2.1914 -- 164 2681 0.1351 0.1636 -- 100.0
X Ray Diffraction 2.1914 2.2558 -- 137 2703 0.1368 0.1809 -- 100.0
X Ray Diffraction 2.2558 2.3286 -- 122 2737 0.1381 0.1544 -- 100.0
X Ray Diffraction 2.3286 2.4118 -- 141 2708 0.1332 0.1646 -- 100.0
X Ray Diffraction 2.4118 2.5083 -- 135 2720 0.1372 0.167 -- 100.0
X Ray Diffraction 2.5083 2.6224 -- 142 2705 0.137 0.1695 -- 100.0
X Ray Diffraction 2.6224 2.7606 -- 139 2727 0.1449 0.184 -- 100.0
X Ray Diffraction 2.7606 2.9335 -- 134 2757 0.146 0.1619 -- 100.0
X Ray Diffraction 2.9335 3.1598 -- 148 2733 0.1403 0.1718 -- 100.0
X Ray Diffraction 3.1598 3.4774 -- 127 2764 0.1446 0.1745 -- 100.0
X Ray Diffraction 3.4774 3.9798 -- 147 2759 0.1355 0.1761 -- 100.0
X Ray Diffraction 3.9798 5.0109 -- 154 2789 0.1279 0.147 -- 100.0
X Ray Diffraction 5.0109 31.6868 -- 176 2909 0.2117 0.2076 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 22.275
Anisotropic B[1][1] -1.644
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.737
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.763
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.005
f_plane_restr 0.005
f_dihedral_angle_d 15.456
f_chiral_restr 0.067
f_angle_d 1.039
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4899
Nucleic Acid Atoms 0
Heterogen Atoms 10
Solvent Atoms 836

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHENIX refinement version: 1.5_2
PDB_EXTRACT data extraction version: 3.005
ADSC data collection version: Quantum
PHASER phasing