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 283 with the SMILES code C[C@@]1(NC(=O)C2=CC=CC=C2N1)C1=CC=NC=C1

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.33 α = 90
b = 72.92 β = 109.57
c = 52.89 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
PIXEL DECTRIS PILATUS 6M -- 2013-07-18
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.1 0.918409 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
1.34 42.71 94.9 0.067 -- -- 3.852 -- 68343 -- -3.0 12.14
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)
1.34 1.43 88.3 0.696 -- 1.87 -- --

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 1.345 42.712 -- 1.38 -- 68343 3418 95.02 -- 0.1364 0.1352 0.1588 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 1.3448 1.3641 -- 109 2071 0.2502 0.3321 -- 72.0
X Ray Diffraction 1.3641 1.3844 -- 140 2647 0.2181 0.2511 -- 94.0
X Ray Diffraction 1.3844 1.4061 -- 140 2671 0.194 0.2428 -- 95.0
X Ray Diffraction 1.4061 1.4291 -- 142 2683 0.1785 0.2345 -- 94.0
X Ray Diffraction 1.4291 1.4538 -- 140 2673 0.1607 0.2059 -- 95.0
X Ray Diffraction 1.4538 1.4802 -- 140 2658 0.1511 0.2126 -- 95.0
X Ray Diffraction 1.4802 1.5087 -- 143 2716 0.1444 0.1656 -- 94.0
X Ray Diffraction 1.5087 1.5395 -- 141 2672 0.1302 0.1809 -- 95.0
X Ray Diffraction 1.5395 1.5729 -- 143 2723 0.1257 0.1747 -- 96.0
X Ray Diffraction 1.5729 1.6095 -- 142 2699 0.1155 0.1663 -- 95.0
X Ray Diffraction 1.6095 1.6498 -- 143 2718 0.1142 0.1487 -- 96.0
X Ray Diffraction 1.6498 1.6944 -- 144 2725 0.1109 0.1426 -- 96.0
X Ray Diffraction 1.6944 1.7442 -- 143 2729 0.1106 0.169 -- 96.0
X Ray Diffraction 1.7442 1.8005 -- 145 2743 0.1031 0.1398 -- 97.0
X Ray Diffraction 1.8005 1.8649 -- 145 2759 0.1062 0.1345 -- 97.0
X Ray Diffraction 1.8649 1.9396 -- 145 2764 0.106 0.1549 -- 97.0
X Ray Diffraction 1.9396 2.0278 -- 145 2748 0.1052 0.1377 -- 97.0
X Ray Diffraction 2.0278 2.1347 -- 146 2768 0.1083 0.131 -- 97.0
X Ray Diffraction 2.1347 2.2685 -- 145 2757 0.1193 0.1317 -- 96.0
X Ray Diffraction 2.2685 2.4436 -- 145 2757 0.1265 0.1466 -- 98.0
X Ray Diffraction 2.4436 2.6895 -- 147 2804 0.136 0.1477 -- 97.0
X Ray Diffraction 2.6895 3.0786 -- 148 2801 0.1403 0.1428 -- 98.0
X Ray Diffraction 3.0786 3.8783 -- 148 2818 0.1518 0.1573 -- 98.0
X Ray Diffraction 3.8783 42.7338 -- 149 2821 0.1583 0.1705 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 15.7022
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_bond_d 0.007
f_dihedral_angle_d 10.92
f_angle_d 1.183
f_chiral_restr 0.07
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2369
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 210

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