X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.6
Temperature 290.0
Details 0.1 M ammonium acetate, 0.1 M sodium acetate, 24-30% PEG 4000; crystal obtained by streak-seeding and soaked with 90 mM of fragment 29 with the SMILES code C[C@H]1CN(C[C@H](O)COC2CCCC2)C[C@@H](C)O1

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.35 α = 90
b = 73.35 β = 109.88
c = 52.91 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 MARMOSAIC 225 mm CCD -- 2012-09-04
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1

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
1.5 42.65 97.8 0.074 -- -- 4.153 -- 51063 -- -3.0 10.83
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)
1.5 1.59 88.1 0.499 -- 2.71 -- --

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 1.5 42.644 -- 1.36 -- 51060 2554 97.91 -- 0.1439 0.142 0.1792 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 1.4999 1.5288 -- 95 1805 0.1724 0.2859 -- 66.0
X Ray Diffraction 1.5288 1.56 -- 145 2748 0.1609 0.2473 -- 100.0
X Ray Diffraction 1.56 1.5939 -- 143 2715 0.1432 0.19 -- 100.0
X Ray Diffraction 1.5939 1.631 -- 145 2757 0.1304 0.2087 -- 100.0
X Ray Diffraction 1.631 1.6717 -- 144 2730 0.1253 0.1781 -- 100.0
X Ray Diffraction 1.6717 1.7169 -- 145 2751 0.1284 0.217 -- 100.0
X Ray Diffraction 1.7169 1.7675 -- 143 2727 0.1267 0.1965 -- 100.0
X Ray Diffraction 1.7675 1.8245 -- 145 2751 0.1244 0.1993 -- 100.0
X Ray Diffraction 1.8245 1.8897 -- 145 2761 0.1245 0.1826 -- 100.0
X Ray Diffraction 1.8897 1.9654 -- 144 2735 0.1308 0.1918 -- 100.0
X Ray Diffraction 1.9654 2.0548 -- 144 2730 0.1285 0.1824 -- 100.0
X Ray Diffraction 2.0548 2.1632 -- 145 2753 0.1282 0.1497 -- 100.0
X Ray Diffraction 2.1632 2.2987 -- 144 2730 0.1343 0.1617 -- 100.0
X Ray Diffraction 2.2987 2.4762 -- 144 2736 0.1445 0.1869 -- 100.0
X Ray Diffraction 2.4762 2.7253 -- 145 2759 0.1469 0.1788 -- 100.0
X Ray Diffraction 2.7253 3.1196 -- 145 2756 0.1554 0.1773 -- 100.0
X Ray Diffraction 3.1196 3.9299 -- 145 2749 0.1587 0.1669 -- 100.0
X Ray Diffraction 3.9299 42.6617 -- 148 2813 0.148 0.1585 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 12.7785
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 10.96
f_angle_d 1.145
f_bond_d 0.008
f_chiral_restr 0.068
f_plane_restr 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2369
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 228

Software

Software
Software Name Purpose
XDS data scaling
PHENIX refinement
PHASER phasing version: 2.5.7
PDB_EXTRACT data extraction version: 3.20
XDS data reduction