1Z67 | pdb_00001z67

Structure of Homeodomain-like Protein of Unknown Function S4005 from Shigella flexneri


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72930.1 M Bis-Tris, 2 M ammonium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
237.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.476α = 90
b = 40.479β = 93.78
c = 48.333γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDSBC-32005-03-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.97934APS19-BM

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
11.454086.50.0439.24.11711117111
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)
11.451.4826.50.332.141.6291

Refinement

Statistics
Diffraction IDStructure Solution 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 DIFFRACTIONSAD1.45401711117111173986.50.16430.16430.16170.18170.20790.188RANDOM22.941
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]
0.62-0.180.57-1.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.405
r_dihedral_angle_3_deg14.39
r_dihedral_angle_4_deg14.281
r_sphericity_free5.69
r_scangle_it4.393
r_dihedral_angle_1_deg4.03
r_sphericity_bonded3.849
r_scbond_it3.084
r_mcangle_it2.166
r_rigid_bond_restr1.958
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.405
r_dihedral_angle_3_deg14.39
r_dihedral_angle_4_deg14.281
r_sphericity_free5.69
r_scangle_it4.393
r_dihedral_angle_1_deg4.03
r_sphericity_bonded3.849
r_scbond_it3.084
r_mcangle_it2.166
r_rigid_bond_restr1.958
r_mcbond_it1.44
r_angle_refined_deg1.427
r_nbtor_refined0.3
r_nbd_refined0.225
r_symmetry_vdw_refined0.19
r_symmetry_hbond_refined0.172
r_xyhbond_nbd_refined0.147
r_chiral_restr0.098
r_bond_refined_d0.017
r_gen_planes_refined0.006
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms939
Nucleic Acid Atoms
Solvent Atoms156
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing