1O5J

Crystal structure of Periplasmic divalent cation tolerance protein (TM1056) from Thermotoga maritima at 1.95 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION,SITTING DROP,NANODROP10.529330% PEG-400, 0.1M CAPS pH 10.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
Crystal Properties
Matthew coefficientSolvent content
2.0539.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.514α = 90
b = 52.514β = 90
c = 34.707γ = 120
Symmetry
Space GroupP 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDAPSwater cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror2002-10-25MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.97944, 0.97924, 0.95658APS19-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.9545.481000.06832.917.49733741.58
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.952.0270.020.2453.73.99563

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMADTHROUGHOUT1.9545.48699333993.940.159070.156030.22061RANDOM39.27
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]
-2.39-1.2-2.393.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.307
r_dihedral_angle_4_deg23.559
r_dihedral_angle_3_deg16.609
r_scangle_it7.133
r_dihedral_angle_1_deg6.361
r_scbond_it5.692
r_mcangle_it3.116
r_mcbond_it2.511
r_angle_refined_deg1.441
r_angle_other_deg0.804
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.307
r_dihedral_angle_4_deg23.559
r_dihedral_angle_3_deg16.609
r_scangle_it7.133
r_dihedral_angle_1_deg6.361
r_scbond_it5.692
r_mcangle_it3.116
r_mcbond_it2.511
r_angle_refined_deg1.441
r_angle_other_deg0.804
r_xyhbond_nbd_refined0.239
r_symmetry_hbond_refined0.232
r_symmetry_vdw_other0.214
r_nbd_refined0.206
r_nbd_other0.193
r_symmetry_vdw_refined0.148
r_chiral_restr0.097
r_nbtor_other0.089
r_bond_refined_d0.018
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms890
Nucleic Acid Atoms
Solvent Atoms74
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEmodel building
REFMACrefinement
RESOLVEphasing