2QSX | pdb_00002qsx

Crystal structure of putative transcriptional regulator LysR From Vibrio parahaemolyticus


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52980.1 M MES Na pH 6.5, 0.8 M Magnesium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.8734.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.291α = 90
b = 83.11β = 90
c = 95.509γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315mirrors2007-02-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97980APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.6462.7599.50.0731.98.6469074557820.532
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.641.799.80.393.78.74635

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT1.6462.754433544335236798.990.206250.206250.20450.20270.239820.2376RANDOM23.283
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.52-0.430.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.317
r_dihedral_angle_4_deg17.288
r_dihedral_angle_3_deg14.933
r_dihedral_angle_1_deg8.562
r_scangle_it3.13
r_scbond_it2.086
r_angle_refined_deg1.526
r_mcangle_it1.506
r_mcbond_it0.958
r_nbtor_refined0.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.317
r_dihedral_angle_4_deg17.288
r_dihedral_angle_3_deg14.933
r_dihedral_angle_1_deg8.562
r_scangle_it3.13
r_scbond_it2.086
r_angle_refined_deg1.526
r_mcangle_it1.506
r_mcbond_it0.958
r_nbtor_refined0.312
r_symmetry_vdw_refined0.233
r_nbd_refined0.202
r_xyhbond_nbd_refined0.2
r_symmetry_hbond_refined0.139
r_chiral_restr0.103
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2982
Nucleic Acid Atoms
Solvent Atoms257
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
MLPHAREphasing