X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.5
Temperature 293.0
Details 0.2 M Li2SO4,0.1 M MgSO4, 0.1 M acetate pH 4.5, and 5% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.87 α = 78.57
b = 46.24 β = 81.8
c = 62.28 γ = 61.11
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 200
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2009-06-03
Diffraction Radiation
Monochromator Protocol
Si 200 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-ID 1 APS 22-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
-- 50 79.7 -- -- -- -- 85025 n/a 1.0 1.0 --
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)
1.29 1.31 76.9 -- -- 3.0 1.7 --

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 1.303 26.207 -- 0.04 65145 80860 4099 75.46 -- 0.175 0.1735 0.202 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 1.3031 1.3185 -- 65 1289 0.151 0.257 -- 36.0
X Ray Diffraction 1.3185 1.3345 -- 76 1507 0.1655 0.207 -- 43.0
X Ray Diffraction 1.3345 1.3514 -- 81 1558 0.1521 0.2293 -- 44.0
X Ray Diffraction 1.3514 1.3692 -- 68 1672 0.1638 0.2049 -- 48.0
X Ray Diffraction 1.3692 1.388 -- 86 1739 0.1659 0.2578 -- 49.0
X Ray Diffraction 1.388 1.4078 -- 85 1842 0.1705 0.2099 -- 53.0
X Ray Diffraction 1.4078 1.4288 -- 93 1940 0.1609 0.2557 -- 55.0
X Ray Diffraction 1.4288 1.4511 -- 98 2052 0.1682 0.1975 -- 59.0
X Ray Diffraction 1.4511 1.4749 -- 116 2103 0.1627 0.2375 -- 60.0
X Ray Diffraction 1.4749 1.5003 -- 103 2310 0.1656 0.22 -- 65.0
X Ray Diffraction 1.5003 1.5276 -- 121 2457 0.1658 0.2103 -- 70.0
X Ray Diffraction 1.5276 1.557 -- 152 2535 0.1678 0.2126 -- 73.0
X Ray Diffraction 1.557 1.5888 -- 156 2644 0.1719 0.2211 -- 76.0
X Ray Diffraction 1.5888 1.6233 -- 158 2774 0.1751 0.2175 -- 80.0
X Ray Diffraction 1.6233 1.6611 -- 176 2939 0.1759 0.2025 -- 84.0
X Ray Diffraction 1.6611 1.7026 -- 144 3048 0.1671 0.2455 -- 87.0
X Ray Diffraction 1.7026 1.7486 -- 184 3096 0.1653 0.2417 -- 89.0
X Ray Diffraction 1.7486 1.8001 -- 180 3223 0.1652 0.1983 -- 92.0
X Ray Diffraction 1.8001 1.8582 -- 163 3236 0.1572 0.19 -- 92.0
X Ray Diffraction 1.8582 1.9246 -- 174 3264 0.1495 0.2055 -- 93.0
X Ray Diffraction 1.9246 2.0016 -- 185 3298 0.142 0.1762 -- 94.0
X Ray Diffraction 2.0016 2.0926 -- 171 3326 0.1483 0.1897 -- 95.0
X Ray Diffraction 2.0926 2.2029 -- 170 3367 0.1424 0.1736 -- 95.0
X Ray Diffraction 2.2029 2.3409 -- 198 3335 0.1547 0.1935 -- 96.0
X Ray Diffraction 2.3409 2.5215 -- 207 3350 0.1655 0.1778 -- 96.0
X Ray Diffraction 2.5215 2.775 -- 174 3379 0.1711 0.231 -- 96.0
X Ray Diffraction 2.775 3.1759 -- 202 3351 0.1648 0.1769 -- 96.0
X Ray Diffraction 3.1759 3.999 -- 160 3284 0.1681 0.1786 -- 93.0
X Ray Diffraction 3.999 26.2122 -- 153 2843 0.2441 0.2355 -- 81.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 9.4878
Anisotropic B[1][2] 1.5095
Anisotropic B[1][3] 2.5509
Anisotropic B[2][2] -3.3393
Anisotropic B[2][3] 1.4012
Anisotropic B[3][3] -6.1484
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.008
f_chiral_restr 0.075
f_dihedral_angle_d 11.946
f_angle_d 1.251
f_bond_d 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3774
Nucleic Acid Atoms 0
Heterogen Atoms 5
Solvent Atoms 357

Software

Computing
Computing Package Purpose
sergui Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
Phaser Structure Solution
PHENIX (phenix.refine: 1.6.4_486) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.6.4_486) refinement
Phaser model building
sergui data collection