5WS4

Crystal structure of tripartite-type ABC transporter MacB from Acinetobacter baumannii


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.2
Temperature 298.0
Details 1.2M Sodium citric acid, 0.1M Sodium HEPES (pH7.2)

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 229.65 α = 90
b = 229.65 β = 90
c = 154.58 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR scanner 300 mm plate -- 2015-05-13
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL44XU 1.750 SPring-8 BL44XU

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
3.4 50 99.9 0.086 -- -- 16.3 -- 46498 -- -- --
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)
3.4 3.46 100.0 -- -- 1.0 15.8 --

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
SAD 3.4 49.115 -- 0.08 -- 46498 2357 81.22 -- 0.2285 0.227 0.2571 --
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 3.4 3.4386 -- 10 488 0.2923 0.1707 -- 14.0
X Ray Diffraction 3.4386 3.4791 -- 39 899 0.2805 0.332 -- 26.0
X Ray Diffraction 3.4791 3.5215 -- 59 1230 0.2676 0.3 -- 36.0
X Ray Diffraction 3.5215 3.5661 -- 61 1413 0.282 0.3457 -- 41.0
X Ray Diffraction 3.5661 3.613 -- 96 1617 0.2618 0.3155 -- 47.0
X Ray Diffraction 3.613 3.6625 -- 90 1844 0.2584 0.3431 -- 54.0
X Ray Diffraction 3.6625 3.7148 -- 98 2070 0.2534 0.2742 -- 60.0
X Ray Diffraction 3.7148 3.7702 -- 119 2237 0.256 0.2527 -- 65.0
X Ray Diffraction 3.7702 3.8291 -- 147 2450 0.2535 0.2914 -- 71.0
X Ray Diffraction 3.8291 3.8918 -- 139 2590 0.2589 0.2845 -- 76.0
X Ray Diffraction 3.8918 3.9589 -- 195 2749 0.2587 0.2791 -- 81.0
X Ray Diffraction 3.9589 4.0309 -- 144 2980 0.2448 0.2325 -- 87.0
X Ray Diffraction 4.0309 4.1084 -- 167 3152 0.2288 0.2492 -- 92.0
X Ray Diffraction 4.1084 4.1922 -- 169 3351 0.2238 0.2551 -- 97.0
X Ray Diffraction 4.1922 4.2833 -- 202 3385 0.2199 0.2453 -- 100.0
X Ray Diffraction 4.2833 4.3829 -- 160 3441 0.2151 0.2805 -- 100.0
X Ray Diffraction 4.3829 4.4924 -- 196 3419 0.2 0.2338 -- 100.0
X Ray Diffraction 4.4924 4.6138 -- 205 3433 0.1964 0.2318 -- 100.0
X Ray Diffraction 4.6138 4.7494 -- 184 3408 0.1823 0.2406 -- 100.0
X Ray Diffraction 4.7494 4.9026 -- 146 3445 0.1865 0.2185 -- 100.0
X Ray Diffraction 4.9026 5.0776 -- 197 3429 0.2139 0.2554 -- 100.0
X Ray Diffraction 5.0776 5.2807 -- 161 3439 0.2085 0.2775 -- 100.0
X Ray Diffraction 5.2807 5.5207 -- 171 3468 0.2263 0.2491 -- 100.0
X Ray Diffraction 5.5207 5.8114 -- 170 3423 0.2321 0.2535 -- 100.0
X Ray Diffraction 5.8114 6.1748 -- 194 3416 0.2422 0.2867 -- 100.0
X Ray Diffraction 6.1748 6.6505 -- 196 3416 0.2388 0.2601 -- 100.0
X Ray Diffraction 6.6505 7.3178 -- 220 3400 0.2282 0.2572 -- 100.0
X Ray Diffraction 7.3178 8.3722 -- 207 3414 0.2116 0.2362 -- 100.0
X Ray Diffraction 8.3722 10.531 -- 186 3418 0.1733 0.1891 -- 100.0
X Ray Diffraction 10.531 49.1198 -- 138 3342 0.2848 0.3165 -- 96.0
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 0.819
f_bond_d 0.004
f_dihedral_angle_d 2.613
f_chiral_restr 0.049
f_plane_restr 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9770
Nucleic Acid Atoms 0
Heterogen Atoms 54
Solvent Atoms 0

Software

Software
Software Name Purpose
PHENIX refinement version: (1.11.1_2575: ???)
HKL-2000 data reduction
SCALEPACK data scaling
SHARP phasing
O model building
Coot model building