X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 298.0
Details 2 M ammonium sulphate, 0.1 M HEPES pH 7.5, 2% PEG 400, virginiamycin M1, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 93.31 α = 90
b = 184.74 β = 90
c = 98.57 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2012-07-27
Diffraction Radiation
Monochromator Protocol
C(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F

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
2.3 30 99.1 -- 0.079 -- 6.0 -- 37898 0.0 -2.0 --
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)
2.3 2.34 100.0 -- 0.576 2.64 5.8 --

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 2.36 29.389 -- 1.34 -- 34991 1751 98.83 -- 0.1865 0.1842 0.2284 --
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 2.36 2.4238 -- 135 2578 0.2193 0.2566 -- 100.0
X Ray Diffraction 2.4238 2.4951 -- 134 2526 0.2133 0.2803 -- 100.0
X Ray Diffraction 2.4951 2.5756 -- 134 2551 0.2167 0.3209 -- 100.0
X Ray Diffraction 2.5756 2.6676 -- 136 2581 0.1987 0.2357 -- 100.0
X Ray Diffraction 2.6676 2.7743 -- 134 2535 0.1943 0.2597 -- 100.0
X Ray Diffraction 2.7743 2.9005 -- 135 2582 0.206 0.263 -- 100.0
X Ray Diffraction 2.9005 3.0532 -- 135 2563 0.1963 0.2603 -- 100.0
X Ray Diffraction 3.0532 3.2443 -- 137 2576 0.2043 0.2524 -- 100.0
X Ray Diffraction 3.2443 3.4944 -- 135 2576 0.1852 0.2276 -- 100.0
X Ray Diffraction 3.4944 3.8454 -- 118 2245 0.1975 0.2746 -- 87.0
X Ray Diffraction 3.8454 4.4002 -- 135 2564 0.1425 0.1595 -- 99.0
X Ray Diffraction 4.4002 5.5378 -- 140 2631 0.1464 0.185 -- 100.0
X Ray Diffraction 5.5378 29.391 -- 143 2732 0.1956 0.2153 -- 100.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.075
f_dihedral_angle_d 15.664
f_angle_d 1.238
f_bond_d 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5094
Nucleic Acid Atoms 0
Heterogen Atoms 196
Solvent Atoms 508

Software

Computing
Computing Package Purpose
HKL-3000 Data Collection
HKL-3000 Data Reduction (intensity integration)
HKL-3000 Data Reduction (data scaling)
PHENIX (phenix.phaser) Structure Solution
PHENIX (phenix.refine: 1.8.1_1168) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8.1_1168) refinement
PHENIX version: (phenix.phaser) model building
HKL-3000 data collection