2HGV

N-terminal GAF domain of transcriptional pleiotropic repressor CodY


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2B18PDB ENTRY 2B18

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7291PEG 5000, calcium acetate, valine, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.1542.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.69α = 90
b = 84.846β = 90
c = 54.929γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2005-04-25MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.9800ESRFBM14

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
12.330990.10413.76.176467646
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)
2.32.3892.20.3614.2672

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2B182.327.72723172313501000.168040.168040.164270.24418RANDOM39.09
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]
-0.010.18-0.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.5
r_dihedral_angle_4_deg16.204
r_dihedral_angle_3_deg15.735
r_dihedral_angle_1_deg5.821
r_scangle_it5.367
r_sphericity_free4.256
r_scbond_it3.738
r_mcangle_it3.701
r_mcbond_it2.83
r_sphericity_bonded1.901
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.5
r_dihedral_angle_4_deg16.204
r_dihedral_angle_3_deg15.735
r_dihedral_angle_1_deg5.821
r_scangle_it5.367
r_sphericity_free4.256
r_scbond_it3.738
r_mcangle_it3.701
r_mcbond_it2.83
r_sphericity_bonded1.901
r_rigid_bond_restr1.677
r_angle_refined_deg1.408
r_mcbond_other0.858
r_angle_other_deg0.819
r_symmetry_hbond_refined0.251
r_symmetry_vdw_other0.249
r_symmetry_vdw_refined0.221
r_nbd_refined0.209
r_nbd_other0.196
r_xyhbond_nbd_refined0.193
r_nbtor_refined0.17
r_nbtor_other0.087
r_chiral_restr0.077
r_bond_refined_d0.013
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1236
Nucleic Acid Atoms
Solvent Atoms131
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing