1O3U

Crystal structure of an hepn domain protein (tm0613) from thermotoga maritima at 1.75 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1829310% PEG 8000; Imidazole pH 8.0; 0.2 M Ca(Ac)2, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K, pH 8.00
Crystal Properties
Matthews coefficientSolvent content
1.7428.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.922α = 90
b = 57.922β = 90
c = 63.735γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC2002-12-11MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.20.97910, 0.97930, 0.91840ALS5.0.2

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
11.7525.90495.60.07616.55.11093527.98
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)
11.751.872.30.4172.22.3

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 DIFFRACTIONMADTHROUGHOUT1.7525.99855107995.50.1850.1790.237RANDOM16.26
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]
-0.44-0.440.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37
r_dihedral_angle_4_deg19.45
r_dihedral_angle_3_deg13.712
r_scangle_it5.162
r_dihedral_angle_1_deg4.846
r_scbond_it3.051
r_mcangle_it1.813
r_angle_refined_deg1.255
r_mcbond_it0.936
r_angle_other_deg0.787
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37
r_dihedral_angle_4_deg19.45
r_dihedral_angle_3_deg13.712
r_scangle_it5.162
r_dihedral_angle_1_deg4.846
r_scbond_it3.051
r_mcangle_it1.813
r_angle_refined_deg1.255
r_mcbond_it0.936
r_angle_other_deg0.787
r_symmetry_vdw_other0.308
r_nbd_other0.235
r_nbd_refined0.211
r_xyhbond_nbd_refined0.194
r_symmetry_vdw_refined0.166
r_symmetry_hbond_refined0.149
r_nbtor_other0.086
r_chiral_restr0.076
r_bond_refined_d0.016
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms963
Nucleic Acid Atoms
Solvent Atoms128
Heterogen Atoms

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
RESOLVEmodel building
SOLVEphasing
REFMACrefinement
CCP4data scaling
RESOLVEphasing