1Y80

Structure of a corrinoid (factor IIIm)-binding protein from Moorella thermoacetica


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1modified microbatch6.72910.1M Sodium HEPES, 1.6M ammonium sulfate, 30% 1,6-hexanediol, pH 6.7, modified microbatch, temperature 291K

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.689α = 90
b = 62.738β = 90
c = 34.543γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.5798APS22-ID

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
11.6500.07713939
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)
11.61.6638.60.216

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 DIFFRACTIONSADTHROUGHOUT1.741.631218452891.510.17570.174250.2101RANDOM14.075
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]
0.32-1.090.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.32
r_dihedral_angle_3_deg10.938
r_dihedral_angle_1_deg4.929
r_dihedral_angle_4_deg3.964
r_scangle_it3.029
r_mcangle_it2.299
r_scbond_it2.077
r_angle_refined_deg1.954
r_mcbond_it1.861
r_angle_other_deg0.753
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.32
r_dihedral_angle_3_deg10.938
r_dihedral_angle_1_deg4.929
r_dihedral_angle_4_deg3.964
r_scangle_it3.029
r_mcangle_it2.299
r_scbond_it2.077
r_angle_refined_deg1.954
r_mcbond_it1.861
r_angle_other_deg0.753
r_mcbond_other0.466
r_symmetry_vdw_other0.231
r_nbd_refined0.205
r_nbd_other0.171
r_nbtor_refined0.162
r_symmetry_vdw_refined0.102
r_xyhbond_nbd_refined0.096
r_nbtor_other0.081
r_symmetry_hbond_refined0.075
r_chiral_restr0.067
r_bond_refined_d0.015
r_gen_planes_refined0.005
r_bond_other_d0.003
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms909
Nucleic Acid Atoms
Solvent Atoms72
Heterogen Atoms96

Software

Software
Software NamePurpose
SOLVEphasing
RESOLVEphasing
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
SHELXDphasing