5IH1

Macrolide 2'-phosphotransferase type II - complex with GDP and phosphorylated josamycin


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 7.5
Temperature 295.0
Details 0.1 M calcium acetate, 0.1M Tris, 25-40% PEG 4000

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 40.37 α = 90
b = 80.87 β = 90
c = 97.87 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-300 -- 2011-08-12
Diffraction Radiation
Monochromator Protocol
DCM SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CLSI BEAMLINE 08ID-1 0.9793 CLSI 08ID-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
1.31 41.11 100.0 0.046 -- -- 4.5 -- 77829 -- -3.0 --
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)
1.31 1.34 100.0 0.661 -- 3.1 -- --

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
-- 1.31 41.867 -- 1.99 -- 77827 3892 99.98 -- 0.1615 0.1606 0.1781 --
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 1.3099 1.3259 -- 135 2567 0.2547 0.2707 -- 100.0
X Ray Diffraction 1.3259 1.3427 -- 140 2648 0.2293 0.2414 -- 100.0
X Ray Diffraction 1.3427 1.3604 -- 136 2597 0.2176 0.2407 -- 100.0
X Ray Diffraction 1.3604 1.379 -- 137 2603 0.2072 0.2215 -- 100.0
X Ray Diffraction 1.379 1.3987 -- 137 2602 0.2117 0.2294 -- 100.0
X Ray Diffraction 1.3987 1.4196 -- 137 2599 0.197 0.2289 -- 100.0
X Ray Diffraction 1.4196 1.4418 -- 139 2640 0.1905 0.17 -- 100.0
X Ray Diffraction 1.4418 1.4654 -- 135 2568 0.1771 0.208 -- 100.0
X Ray Diffraction 1.4654 1.4907 -- 138 2627 0.1738 0.1938 -- 100.0
X Ray Diffraction 1.4907 1.5178 -- 137 2590 0.1697 0.1818 -- 100.0
X Ray Diffraction 1.5178 1.547 -- 140 2664 0.1755 0.1843 -- 100.0
X Ray Diffraction 1.547 1.5785 -- 135 2573 0.1666 0.1959 -- 100.0
X Ray Diffraction 1.5785 1.6129 -- 140 2645 0.1578 0.1964 -- 100.0
X Ray Diffraction 1.6129 1.6504 -- 137 2617 0.1556 0.1724 -- 100.0
X Ray Diffraction 1.6504 1.6917 -- 139 2636 0.1534 0.1556 -- 100.0
X Ray Diffraction 1.6917 1.7374 -- 138 2623 0.1582 0.1683 -- 100.0
X Ray Diffraction 1.7374 1.7885 -- 138 2629 0.1579 0.1885 -- 100.0
X Ray Diffraction 1.7885 1.8462 -- 139 2642 0.1659 0.1769 -- 100.0
X Ray Diffraction 1.8462 1.9122 -- 138 2607 0.1583 0.1896 -- 100.0
X Ray Diffraction 1.9122 1.9888 -- 140 2656 0.1531 0.1737 -- 100.0
X Ray Diffraction 1.9888 2.0793 -- 140 2670 0.151 0.1897 -- 100.0
X Ray Diffraction 2.0793 2.1889 -- 138 2620 0.1482 0.1816 -- 100.0
X Ray Diffraction 2.1889 2.3261 -- 140 2663 0.1484 0.1661 -- 100.0
X Ray Diffraction 2.3261 2.5056 -- 141 2678 0.1441 0.156 -- 100.0
X Ray Diffraction 2.5056 2.7577 -- 140 2662 0.1551 0.1623 -- 100.0
X Ray Diffraction 2.7577 3.1567 -- 143 2712 0.1632 0.1989 -- 100.0
X Ray Diffraction 3.1567 3.9766 -- 143 2728 0.1496 0.1409 -- 100.0
X Ray Diffraction 3.9766 41.8882 -- 152 2869 0.1634 0.1881 -- 100.0
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 13.698
f_plane_restr 0.006
f_angle_d 1.357
f_bond_d 0.009
f_chiral_restr 0.069
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2401
Nucleic Acid Atoms 0
Heterogen Atoms 92
Solvent Atoms 500

Software

Software
Software Name Purpose
PHENIX refinement version: dev_1627
XSCALE data scaling
PDB_EXTRACT data extraction version: 3.20