2XG8

Structural basis of gene regulation by protein PII: The crystal complex of PII and PipX from Synechococcus elongatus PCC 7942


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5PII-PIPX COMPLEX AT 5.5 MG/ML IN 20 MM HEPES PH 7.5, 1MM DTT, 0.4 M NACL, 5 MM MAGNESIUM CHLORIDE. PRECIPITANT SOLUTION: 15 % PEG 3.35K, 0.2 M SODIUM FORMATE.
Crystal Properties
Matthews coefficientSolvent content
2.1943.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.383α = 90
b = 61.585β = 126.44
c = 112.979γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2007-11-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

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
13.290.999.90.117.13.9103301.874.4
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)
133.3799.90.421.83.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1V5H, CHAIN J3.250982949599.830.229230.227080.27247RANDOM70.104
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]
1.511.60.050.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.799
r_dihedral_angle_3_deg17.696
r_dihedral_angle_4_deg14.408
r_dihedral_angle_1_deg8.25
r_angle_refined_deg1.259
r_angle_other_deg1.009
r_scangle_it0.763
r_scbond_it0.475
r_mcangle_it0.375
r_mcbond_it0.337
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.799
r_dihedral_angle_3_deg17.696
r_dihedral_angle_4_deg14.408
r_dihedral_angle_1_deg8.25
r_angle_refined_deg1.259
r_angle_other_deg1.009
r_scangle_it0.763
r_scbond_it0.475
r_mcangle_it0.375
r_mcbond_it0.337
r_symmetry_hbond_refined0.3
r_symmetry_vdw_refined0.244
r_symmetry_vdw_other0.236
r_nbd_refined0.228
r_nbd_other0.192
r_nbtor_refined0.181
r_chiral_restr0.142
r_xyhbond_nbd_refined0.122
r_nbtor_other0.083
r_mcbond_other0.031
r_bond_refined_d0.008
r_bond_other_d0.003
r_gen_planes_refined0.003
r_gen_planes_other0.002
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4529
Nucleic Acid Atoms
Solvent Atoms3
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing