3FTJ

Crystal structure of the periplasmic region of MacB from Actinobacillus actinomycetemcomitans


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 287.0
Details 0.1M HEPES pH 7.5, 1% PEG 400, 2.0M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 287K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 108.44 α = 90
b = 108.44 β = 90
c = 92.89 γ = 120
Symmetry
Space Group H 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 173
2 173
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 double mirror 2008-05-05
CCD ADSC QUANTUM 315 -- 2008-06-15
Diffraction Radiation
Monochromator Protocol
sillicon crystal, double mirror SINGLE WAVELENGTH
-- MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PAL/PLS BEAMLINE 4A 1.0000 PAL/PLS 4A
SYNCHROTRON PAL/PLS BEAMLINE 4A 0.97943, 0.97963, 0.97175 PAL/PLS 4A

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 50 96.3 0.08 0.08 -- 5.2 14360 13829 0.0 0.0 12.1
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)
2.0 2.07 76.0 0.321 0.321 2.1 2.6 1075

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
MAD 1.999 33.158 0.0 2.12 14360 13828 694 50.13 -- 0.202 0.1995 0.25 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 1.9992 2.1536 -- 125 2265 0.258 0.3274 -- 44.0
X Ray Diffraction 2.1536 2.3703 -- 140 2654 0.2145 0.2634 -- 51.0
X Ray Diffraction 2.3703 2.7131 -- 147 2681 0.2061 0.248 -- 51.0
X Ray Diffraction 2.7131 3.4177 -- 151 2705 0.1925 0.2486 -- 52.0
X Ray Diffraction 3.4177 33.1627 -- 131 2829 0.183 0.2205 -- 53.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 31.375
Anisotropic B[1][1] 1.817
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.817
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.634
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_angle_d 0.958
f_dihedral_angle_d 17.604
f_bond_d 0.006
f_chiral_restr 0.066
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.25
Luzzati Sigma A (Observed) 0.27
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.32
Luzzati Sigma A (R-Free Set) 0.28
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1649
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 139

Software

Software
Software Name Purpose
ADSC data collection version: Quantum
SOLVE phasing
CNS refinement version: 1.2
HKL-2000 data reduction
HKL-2000 data scaling
PHENIX refinement