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 117 with the SMILES code N\C(=N/O)C1=CC(Br)=CC=C1

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.29 α = 90
b = 73.08 β = 109.52
c = 52.8 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 -- 2013-01-23
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.2 0.91841 BESSY 14.2

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
1.52 42.69 97.2 0.102 -- -- 4.195 -- 48823 -- -3.0 10.01
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)
1.52 1.61 94.4 0.64 -- 2.34 -- --

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 1.518 22.272 -- 1.99 -- 48811 2441 97.44 -- 0.1601 0.1582 0.1965 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 1.5179 1.5489 -- 137 2590 0.2037 0.2891 -- 93.0
X Ray Diffraction 1.5489 1.5826 -- 141 2681 0.1894 0.2738 -- 97.0
X Ray Diffraction 1.5826 1.6194 -- 144 2730 0.1839 0.237 -- 97.0
X Ray Diffraction 1.6194 1.6599 -- 141 2693 0.1754 0.2417 -- 97.0
X Ray Diffraction 1.6599 1.7047 -- 143 2714 0.1685 0.2677 -- 98.0
X Ray Diffraction 1.7047 1.7549 -- 144 2725 0.1626 0.2481 -- 97.0
X Ray Diffraction 1.7549 1.8115 -- 142 2711 0.1528 0.2247 -- 98.0
X Ray Diffraction 1.8115 1.8762 -- 145 2740 0.1434 0.208 -- 98.0
X Ray Diffraction 1.8762 1.9513 -- 143 2715 0.1303 0.1648 -- 98.0
X Ray Diffraction 1.9513 2.04 -- 144 2739 0.1289 0.1904 -- 98.0
X Ray Diffraction 2.04 2.1475 -- 143 2731 0.1321 0.168 -- 98.0
X Ray Diffraction 2.1475 2.2819 -- 144 2735 0.1406 0.1942 -- 98.0
X Ray Diffraction 2.2819 2.4579 -- 145 2752 0.1514 0.2057 -- 98.0
X Ray Diffraction 2.4579 2.7049 -- 146 2769 0.1634 0.1758 -- 98.0
X Ray Diffraction 2.7049 3.0954 -- 145 2760 0.161 0.1987 -- 99.0
X Ray Diffraction 3.0954 3.8965 -- 146 2776 0.1646 0.1715 -- 99.0
X Ray Diffraction 3.8965 22.2744 -- 148 2809 0.1705 0.1699 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 12.6794
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.054
f_dihedral_angle_d 10.928
f_bond_d 0.009
f_angle_d 1.19
f_plane_restr 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2369
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 164

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