3Q16

Linkage between the Bacterial Acid Stress and Stringent Responses: The Structure of the Inducible Lysine Decarboxylase


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 285.0
Details 0.1 M Tris, 0.1 M ammonium bromide, 25-35% PEG1000, 0-10% glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 270.29 α = 90
b = 181.29 β = 125.06
c = 169.93 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 130 mm -- 2009-12-12
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CLSI BEAMLINE 08ID-1 -- CLSI 08ID-1

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
4.1 140.23 77.4 0.219 0.219 -- 2.7 52673 40852 -- -- --
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)
4.1 4.32 79.3 0.421 0.421 1.7 2.6 --

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 4.1 68.0 -- -- -- 38774 2077 77.58 -- 0.27771 0.27629 0.30432 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 4.1 4.206 -- 144 2941 0.317 0.296 -- 79.55
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 100.395
Anisotropic B[1][1] 3.45
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -2.94
Anisotropic B[2][2] -0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -6.82
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_hbond_refined 0.118
r_mcbond_it 0.107
r_mcangle_it 0.191
r_bond_refined_d 0.005
r_nbtor_refined 0.293
r_scbond_it 0.069
r_chiral_restr 0.046
r_scangle_it 0.131
r_dihedral_angle_4_deg 8.446
r_dihedral_angle_1_deg 3.429
r_dihedral_angle_2_deg 31.809
r_angle_refined_deg 0.766
r_gen_planes_refined 0.003
r_dihedral_angle_3_deg 13.396
r_nbd_refined 0.152
r_xyhbond_nbd_refined 0.096
r_symmetry_vdw_refined 0.126
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 28485
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 0

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
MxDC data collection
MOSFLM data reduction
SCALA data scaling
REFMAC phasing version: 5.2.0019