2F06

Crystal structure of protein BT0572 from Bacteroides thetaiotaomicron


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 291.0
Details 8% PEG 6000, 0.1M Mes pH 6.5, 20% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 64.62 α = 90
b = 64.62 β = 90
c = 244.94 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2005-10-06
Diffraction Radiation
Monochromator Protocol
double crystal MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97940 0.97954, 0.97172 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
2.1 50 99.6 0.086 -- -- 21.3 18814 18739 -- -3.0 --
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)
2.1 2.18 98.7 0.476 -- 4.3 15.7 1782

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 2.1 50.0 -- 0.0 18628 18628 953 99.71 0.20481 0.20481 0.20252 0.24941 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 2.1 2.154 -- 87 1249 0.241 0.349 -- 98.38
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 46.512
Anisotropic B[1][1] 0.02
Anisotropic B[1][2] 0.01
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.02
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.02
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_4_deg 20.578
r_scangle_it 5.072
r_nbd_refined 0.256
r_gen_planes_refined 0.01
r_angle_refined_deg 2.253
r_dihedral_angle_2_deg 39.557
r_dihedral_angle_1_deg 14.748
r_mcbond_it 1.415
r_bond_refined_d 0.026
r_symmetry_hbond_refined 0.341
r_chiral_restr 0.267
r_nbtor_refined 0.312
r_symmetry_vdw_refined 0.313
r_dihedral_angle_3_deg 17.696
r_xyhbond_nbd_refined 0.211
r_scbond_it 3.651
r_mcangle_it 1.985
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2191
Nucleic Acid Atoms 0
Heterogen Atoms 22
Solvent Atoms 85

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0005
HKL-2000 data reduction
SCALEPACK data scaling
HKL-3000 phasing
SHELXD phasing
SHELXE model building
MLPHARE phasing
DM phasing
SOLVE phasing
RESOLVE phasing
O model building
Coot model building
CCP4 phasing