X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.5
Temperature 277.0
Details 0.1 M sodium acetate, pH 4.5, 30% (w/v) PEG-6000, 0.3 M LiSO4, 3% (w/v) TMAO, 50 mM 2-mercaptoethanol, 50 mM 2-hydroxyethyl disulfide, vapor diffusion, hanging drop, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 48.63 α = 90
b = 75.14 β = 93.18
c = 52.72 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2012-06-02
Diffraction Radiation
Monochromator Protocol
two flat Si(111) crystals, mounted in a model DCM from Khozu SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.3.1 1.116 ALS 8.3.1

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
1.58 48.56 97.0 0.051 -- -- -- -- 50324 -- -3.0 21.265
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)
1.58 1.67 91.9 0.378 -- 2.32 -- --

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 1.58 48.555 -- 1.99 -- 50322 2006 97.02 -- 0.1758 0.1747 0.2017 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 1.58 1.6195 -- 132 3058 0.2825 0.3398 -- 86.0
X Ray Diffraction 1.6195 1.6633 -- 139 3404 0.2513 0.2633 -- 96.0
X Ray Diffraction 1.6633 1.7123 -- 150 3512 0.23 0.2992 -- 99.0
X Ray Diffraction 1.7123 1.7675 -- 143 3514 0.2042 0.2608 -- 99.0
X Ray Diffraction 1.7675 1.8307 -- 144 3542 0.1813 0.2066 -- 99.0
X Ray Diffraction 1.8307 1.904 -- 143 3507 0.1658 0.2055 -- 99.0
X Ray Diffraction 1.904 1.9907 -- 147 3507 0.1626 0.207 -- 99.0
X Ray Diffraction 1.9907 2.0956 -- 149 3505 0.1635 0.1845 -- 99.0
X Ray Diffraction 2.0956 2.2269 -- 144 3507 0.1561 0.1941 -- 99.0
X Ray Diffraction 2.2269 2.3988 -- 148 3484 0.16 0.2132 -- 98.0
X Ray Diffraction 2.3988 2.6402 -- 145 3475 0.1636 0.2026 -- 98.0
X Ray Diffraction 2.6402 3.0222 -- 145 3458 0.1767 0.1845 -- 97.0
X Ray Diffraction 3.0222 3.8075 -- 139 3432 0.1618 0.1752 -- 96.0
X Ray Diffraction 3.8075 48.5779 -- 138 3411 0.1675 0.1711 -- 94.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 16.1224
Anisotropic B[1][1] 1.4231
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.7275
Anisotropic B[2][2] -0.5952
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.8279
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 13.464
f_plane_restr 0.008
f_chiral_restr 0.106
f_angle_d 1.564
f_bond_d 0.017
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2739
Nucleic Acid Atoms 0
Heterogen Atoms 86
Solvent Atoms 302

Software

Computing
Computing Package Purpose
BLU-ICE Data Collection
XSCALE Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (phenix.refine: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Xscale data reduction