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 72 with the SMILES code CC1=C(SC(=C1C)C1=NN=CN1)C#N

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.35 α = 90
b = 73.02 β = 109.49
c = 52.71 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 -- 2012-11-16
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
1.3 42.75 99.5 0.058 -- -- 4.178 -- 79297 -- -3.0 9.23
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)
1.3 1.38 98.8 0.563 -- 2.36 -- --

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 1.3 41.08 -- 2.0 -- 79294 3964 99.65 -- 0.134 0.133 0.1524 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 1.2996 1.3154 -- 137 2618 0.2033 0.2251 -- 98.0
X Ray Diffraction 1.3154 1.3321 -- 141 2672 0.1838 0.2422 -- 99.0
X Ray Diffraction 1.3321 1.3496 -- 141 2671 0.1854 0.1868 -- 99.0
X Ray Diffraction 1.3496 1.3681 -- 140 2672 0.1702 0.246 -- 99.0
X Ray Diffraction 1.3681 1.3876 -- 143 2717 0.1591 0.2162 -- 100.0
X Ray Diffraction 1.3876 1.4084 -- 140 2657 0.1545 0.1771 -- 99.0
X Ray Diffraction 1.4084 1.4304 -- 141 2675 0.1445 0.1466 -- 100.0
X Ray Diffraction 1.4304 1.4538 -- 141 2680 0.1355 0.1626 -- 100.0
X Ray Diffraction 1.4538 1.4789 -- 139 2638 0.1294 0.1817 -- 100.0
X Ray Diffraction 1.4789 1.5058 -- 144 2729 0.1272 0.1613 -- 100.0
X Ray Diffraction 1.5058 1.5347 -- 139 2658 0.1192 0.1622 -- 100.0
X Ray Diffraction 1.5347 1.5661 -- 143 2709 0.1192 0.1567 -- 100.0
X Ray Diffraction 1.5661 1.6001 -- 140 2667 0.1104 0.1446 -- 100.0
X Ray Diffraction 1.6001 1.6373 -- 143 2703 0.1064 0.1578 -- 100.0
X Ray Diffraction 1.6373 1.6783 -- 141 2684 0.1004 0.1187 -- 100.0
X Ray Diffraction 1.6783 1.7237 -- 141 2678 0.0998 0.1282 -- 100.0
X Ray Diffraction 1.7237 1.7744 -- 142 2698 0.102 0.1389 -- 100.0
X Ray Diffraction 1.7744 1.8317 -- 142 2701 0.1024 0.1217 -- 100.0
X Ray Diffraction 1.8317 1.8971 -- 142 2688 0.1049 0.1356 -- 100.0
X Ray Diffraction 1.8971 1.9731 -- 143 2716 0.1061 0.1262 -- 100.0
X Ray Diffraction 1.9731 2.0629 -- 141 2681 0.1071 0.1403 -- 100.0
X Ray Diffraction 2.0629 2.1716 -- 142 2706 0.11 0.1257 -- 100.0
X Ray Diffraction 2.1716 2.3077 -- 142 2692 0.1197 0.1338 -- 100.0
X Ray Diffraction 2.3077 2.4858 -- 142 2700 0.1281 0.1488 -- 100.0
X Ray Diffraction 2.4858 2.736 -- 142 2705 0.1373 0.1646 -- 100.0
X Ray Diffraction 2.736 3.1317 -- 143 2718 0.1446 0.1612 -- 100.0
X Ray Diffraction 3.1317 3.9452 -- 143 2718 0.1554 0.1773 -- 100.0
X Ray Diffraction 3.9452 41.1003 -- 146 2779 0.1624 0.1319 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 12.1579
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.072
f_bond_d 0.007
f_plane_restr 0.006
f_dihedral_angle_d 10.68
f_angle_d 1.2
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2369
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 247

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