2R48

Crystal structure of the fructose specific IIB subunit of PTS system from Bacillus subtilis subsp. subtilis str. 168


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 291.0
Details 0.2 M Sodium citrate tribasic dihydrate, 20% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 48.93 α = 90
b = 48.93 β = 90
c = 68.25 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 ADSC QUANTUM 315 mirrors 2007-08-03
Diffraction Radiation
Monochromator Protocol
double crystal MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97950, 0.97960 APS 19-ID

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
1.8 40 95.0 0.07 -- -- 7.0 7790 7790 0.0 0.0 --
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)
1.8 1.85 61.7 0.378 -- 3.3 4.7 --

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 1.8 39.78 -- -- 7785 7402 361 95.19 0.1871 0.18601 0.18328 0.23743 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 1.8 1.847 -- 13 359 0.256 0.331 -- 65.03
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.628
Anisotropic B[1][1] 1.57
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.57
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.13
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 37.292
r_xyhbond_nbd_refined 0.201
r_symmetry_vdw_refined 0.229
r_scangle_it 3.519
r_nbd_refined 0.203
r_chiral_restr 0.092
r_mcbond_it 1.171
r_symmetry_hbond_refined 0.135
r_bond_refined_d 0.019
r_nbtor_refined 0.171
r_angle_other_deg 1.033
r_dihedral_angle_3_deg 13.805
r_nbd_other 0.207
r_bond_other_d 0.011
r_mcbond_other 0.267
r_nbtor_other 0.089
r_mcangle_it 1.417
r_gen_planes_refined 0.006
r_angle_refined_deg 1.712
r_symmetry_vdw_other 0.248
r_gen_planes_other 0.001
r_dihedral_angle_4_deg 14.832
r_dihedral_angle_1_deg 5.461
r_scbond_it 2.453
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 795
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 57

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
SBC-Collect data collection
HKL-3000 data reduction
HKL-3000 data scaling
HKL-3000 phasing
SHELXD phasing
SHELXE model building
MLPHARE phasing
DM phasing
SOLVE phasing
RESOLVE phasing
ARP/wARP model building
CCP4 phasing
Coot model building