3PNB

Phosphopantetheine Adenylyltransferase from Mycobacterium tuberculosis in complex with coenzyme A


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 298.0
Details 0.1 M Tris base, pH 8, 0.15 M magnesium formate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 114.46 α = 90
b = 114.46 β = 90
c = 134.47 γ = 120
Symmetry
Space Group P 3 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 77
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2009-10-21
Diffraction Radiation
Monochromator Protocol
C(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 APS 21-ID-G

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
2.11 50 100.0 0.107 -- -- 10.7 59228 59228 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)
2.11 2.15 100.0 0.547 -- 3.9 9.4 --

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 2.11 50.0 -- -- 59228 53413 2827 94.95 -- 0.21624 0.21458 0.24839 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 2.108 2.163 -- 183 3820 0.263 0.349 -- 92.68
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.995
Anisotropic B[1][1] -0.16
Anisotropic B[1][2] -0.08
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.16
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.24
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_3_deg 12.15
r_scbond_it 1.05
r_gen_planes_refined 0.003
r_dihedral_angle_4_deg 13.416
r_scangle_it 1.951
r_dihedral_angle_1_deg 4.201
r_dihedral_angle_2_deg 28.352
r_mcangle_it 0.79
r_angle_refined_deg 1.003
r_bond_refined_d 0.006
r_chiral_restr 0.061
r_mcbond_it 0.419
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4800
Nucleic Acid Atoms 0
Heterogen Atoms 192
Solvent Atoms 372

Software

Software
Software Name Purpose
MD2 data collection version: diffractometer software from EMBL (with LS-CAT developed extensions)
PHASER phasing version: CCP4
REFMAC refinement version: 5.5.0072
HKL-2000 data reduction
HKL-2000 data scaling