X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.6
Temperature 277.0
Details 8% PEG 4000, 0.1 M Sodium Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 58.13 α = 90
b = 109.79 β = 90
c = 141.67 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 -- 2010-06-11
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL7-1 0.97946 SSRL BL7-1

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
1.6 50 99.1 0.052 0.052 -- 3.6 119994 118914 -3.0 -3.0 18.16
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 1.64 98.6 0.367 0.367 2.6 3.7 8625

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 19.955 -- 1.34 -- 118766 5936 98.91 -- 0.1624 0.1611 0.1869 --
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 1.6182 -- 207 3682 0.2417 0.2748 -- 98.0
X Ray Diffraction 1.6182 1.6372 -- 193 3667 0.2378 0.2864 -- 98.0
X Ray Diffraction 1.6372 1.6572 -- 208 3710 0.2132 0.2503 -- 98.0
X Ray Diffraction 1.6572 1.6781 -- 175 3696 0.2078 0.2456 -- 98.0
X Ray Diffraction 1.6781 1.7002 -- 200 3713 0.1996 0.2265 -- 98.0
X Ray Diffraction 1.7002 1.7235 -- 220 3700 0.1966 0.2353 -- 99.0
X Ray Diffraction 1.7235 1.7481 -- 191 3695 0.1854 0.2154 -- 98.0
X Ray Diffraction 1.7481 1.7742 -- 200 3726 0.1701 0.1978 -- 99.0
X Ray Diffraction 1.7742 1.8019 -- 191 3685 0.1664 0.196 -- 99.0
X Ray Diffraction 1.8019 1.8314 -- 188 3748 0.1632 0.2035 -- 99.0
X Ray Diffraction 1.8314 1.863 -- 201 3702 0.161 0.2144 -- 99.0
X Ray Diffraction 1.863 1.8968 -- 200 3733 0.1533 0.2012 -- 99.0
X Ray Diffraction 1.8968 1.9333 -- 177 3778 0.1602 0.1829 -- 99.0
X Ray Diffraction 1.9333 1.9727 -- 208 3726 0.1531 0.1865 -- 99.0
X Ray Diffraction 1.9727 2.0155 -- 224 3725 0.1532 0.1832 -- 99.0
X Ray Diffraction 2.0155 2.0624 -- 230 3709 0.1566 0.1761 -- 99.0
X Ray Diffraction 2.0624 2.1139 -- 191 3764 0.1567 0.1899 -- 99.0
X Ray Diffraction 2.1139 2.171 -- 172 3777 0.1556 0.1854 -- 99.0
X Ray Diffraction 2.171 2.2348 -- 197 3802 0.1501 0.1686 -- 99.0
X Ray Diffraction 2.2348 2.3068 -- 210 3757 0.1507 0.181 -- 99.0
X Ray Diffraction 2.3068 2.3891 -- 231 3769 0.1525 0.1879 -- 100.0
X Ray Diffraction 2.3891 2.4846 -- 198 3765 0.1575 0.1767 -- 100.0
X Ray Diffraction 2.4846 2.5975 -- 177 3838 0.1607 0.1828 -- 100.0
X Ray Diffraction 2.5975 2.7341 -- 211 3799 0.1595 0.1812 -- 100.0
X Ray Diffraction 2.7341 2.9049 -- 197 3850 0.1619 0.191 -- 100.0
X Ray Diffraction 2.9049 3.1284 -- 190 3813 0.1636 0.1859 -- 100.0
X Ray Diffraction 3.1284 3.4418 -- 197 3861 0.1569 0.1658 -- 99.0
X Ray Diffraction 3.4418 3.9365 -- 185 3741 0.1442 0.1784 -- 97.0
X Ray Diffraction 3.9365 4.9471 -- 186 3938 0.1414 0.1535 -- 100.0
X Ray Diffraction 4.9471 19.9565 -- 181 3961 0.1805 0.2 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -0.2325
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0861
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.1464
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.073
f_dihedral_angle_d 12.83
f_angle_d 1.083
f_bond_d 0.006
Coordinate Error
Parameter Value
Luzzati Sigma A (Observed) 0.41
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6177
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 968

Software

Computing
Computing Package Purpose
BLU-ICE Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.1_743) refinement
PHASER model building
BLU-ICE data collection