6PI4

Crystal structure of ATP synthase epsion chain ATP synthase epsilon chain (ATP synthase F1 sector epsilon subunit) (F-ATPase epsilon subunit) from Mycobacterium smegmatis


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 290.0
Details RigakuReagents JCSG+ screen, B10: 50% PEG 200, 200mM MgCl2, 100mM sodium cacodylate pH 6.5: MysmA.18337.a.B1.PS38196 at 17.3mg/ml + 6mM MgCl2 + 6mM ATP. Cryo: direct: tray 290121 B10: puck nww5-5

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 53.87 α = 90
b = 75.32 β = 90
c = 71.02 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 RAYONIX MX-300 -- 2017-11-09
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
2.1 43.82 99.1 0.054 -- -- 6.101 -- 8662 -- -- 48.139
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)
2.1 2.15 98.9 0.538 -- 3.48 6.225 --

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 2.1 43.817 -- 1.35 -- 8631 862 98.78 -- 0.2261 0.22 0.2831 0
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 2.1 2.2316 -- 160 1274 0.3366 0.3954 0.0 99.0
X Ray Diffraction 2.2316 2.4039 -- 156 1233 0.2952 0.384 0.0 99.0
X Ray Diffraction 2.4039 2.6458 -- 119 1300 0.2836 0.338 0.0 99.0
X Ray Diffraction 2.6458 3.0285 -- 134 1300 0.2511 0.2951 0.0 99.0
X Ray Diffraction 3.0285 3.8153 -- 150 1301 0.2164 0.2658 0.0 99.0
X Ray Diffraction 3.8153 43.8261 -- 143 1361 0.1785 0.2489 0.0 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 70.012
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.007
f_chiral_restr 0.055
f_dihedral_angle_d 17.593
f_angle_d 0.806
f_plane_restr 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 876
Nucleic Acid Atoms 0
Heterogen Atoms 5
Solvent Atoms 26

Software

Software
Software Name Purpose
XDS data reduction
XSCALE data scaling
PHENIX refinement version: (dev_3500)
PDB_EXTRACT data extraction version: 3.25
MR-Rosetta phasing
Coot model building