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 206 with the SMILES code NCC1=CC=C(O1)C(F)(F)F

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.39 α = 90
b = 72.88 β = 109.6
c = 52.83 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 MAR CCD 165 mm -- 2013-04-18
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.3 0.8944 BESSY 14.3

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
1.45 50 99.2 0.078 -- 16.5 3.5 -- 57009 -- -- 9.38
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)
1.45 1.48 99.9 0.476 -- -- 3.4 2868

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 1.448 26.835 -- 1.36 -- 56984 2896 98.95 -- 0.1426 0.1408 0.1766 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 1.4482 1.472 -- 136 2465 0.1666 0.2377 -- 95.0
X Ray Diffraction 1.472 1.4974 -- 125 2573 0.1597 0.2087 -- 100.0
X Ray Diffraction 1.4974 1.5246 -- 123 2593 0.1395 0.205 -- 100.0
X Ray Diffraction 1.5246 1.5539 -- 138 2625 0.1337 0.1968 -- 100.0
X Ray Diffraction 1.5539 1.5856 -- 129 2581 0.1272 0.1838 -- 100.0
X Ray Diffraction 1.5856 1.6201 -- 145 2607 0.1213 0.1762 -- 100.0
X Ray Diffraction 1.6201 1.6578 -- 128 2566 0.1217 0.1789 -- 100.0
X Ray Diffraction 1.6578 1.6992 -- 138 2609 0.1191 0.1618 -- 100.0
X Ray Diffraction 1.6992 1.7452 -- 153 2575 0.1205 0.1824 -- 100.0
X Ray Diffraction 1.7452 1.7965 -- 140 2575 0.1192 0.166 -- 100.0
X Ray Diffraction 1.7965 1.8545 -- 153 2556 0.1239 0.1744 -- 100.0
X Ray Diffraction 1.8545 1.9208 -- 124 2628 0.1178 0.1617 -- 100.0
X Ray Diffraction 1.9208 1.9976 -- 134 2605 0.1168 0.1641 -- 100.0
X Ray Diffraction 1.9976 2.0885 -- 150 2576 0.1221 0.1584 -- 99.0
X Ray Diffraction 2.0885 2.1986 -- 131 2588 0.1254 0.1508 -- 99.0
X Ray Diffraction 2.1986 2.3363 -- 143 2561 0.1359 0.1495 -- 99.0
X Ray Diffraction 2.3363 2.5165 -- 156 2575 0.1402 0.1862 -- 99.0
X Ray Diffraction 2.5165 2.7695 -- 155 2552 0.1453 0.1701 -- 99.0
X Ray Diffraction 2.7695 3.1697 -- 134 2570 0.1509 0.1836 -- 98.0
X Ray Diffraction 3.1697 3.9914 -- 134 2556 0.1641 0.1987 -- 97.0
X Ray Diffraction 3.9914 26.8398 -- 127 2552 0.1708 0.1713 -- 95.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 11.1413
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.17
f_chiral_restr 0.068
f_dihedral_angle_d 10.863
f_bond_d 0.007
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 201

Software

Software
Software Name Purpose
XDS data scaling
PHENIX refinement
PHASER phasing version: 2.5.7
PDB_EXTRACT data extraction version: 3.20
HKL-2000 data reduction