9S6C | pdb_00009s6c

B12 Binding protein - BtuK1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5294.152mM Lanthanides, 0.1M Buffer systems 4 (MOPSO, Bis-Tris) (pH 6.5), 32.5% v/v Precipitant Mix 6 (25% w/v PEG 4000, 40% w/v 1,2,6 Hexanetriol)
Crystal Properties
Matthews coefficientSolvent content
2.5150.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.739α = 90
b = 129.984β = 90
c = 164.66γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2025-07-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.87313ESRFID30B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
11.6546.8596.2111.41131196
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.710.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.81714.28799154499196.3070.1640.16250.16430.19170.195434.173
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]
0.527-0.5980.071
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg14.9
r_dihedral_angle_other_2_deg12.241
r_dihedral_angle_3_deg11.669
r_dihedral_angle_1_deg8.362
r_dihedral_angle_2_deg8.173
r_lrange_it5.779
r_lrange_other5.638
r_scangle_it3.933
r_scangle_other3.932
r_scbond_it2.536
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg14.9
r_dihedral_angle_other_2_deg12.241
r_dihedral_angle_3_deg11.669
r_dihedral_angle_1_deg8.362
r_dihedral_angle_2_deg8.173
r_lrange_it5.779
r_lrange_other5.638
r_scangle_it3.933
r_scangle_other3.932
r_scbond_it2.536
r_scbond_other2.534
r_angle_refined_deg2.15
r_mcangle_it2.107
r_mcangle_other2.107
r_mcbond_it1.552
r_mcbond_other1.55
r_angle_other_deg1.386
r_nbtor_refined0.15
r_nbd_refined0.138
r_chiral_restr0.123
r_symmetry_nbd_refined0.114
r_symmetry_nbd_other0.112
r_nbd_other0.112
r_symmetry_xyhbond_nbd_refined0.111
r_xyhbond_nbd_refined0.109
r_ncsr_local_group_10.083
r_ncsr_local_group_30.08
r_ncsr_local_group_20.077
r_symmetry_nbtor_other0.058
r_gen_planes_refined0.014
r_bond_refined_d0.012
r_bond_other_d0.009
r_gen_planes_other0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7939
Nucleic Acid Atoms
Solvent Atoms642
Heterogen Atoms279

Software

Software
Software NamePurpose
Aimlessdata scaling
gemmidata extraction
REFMACrefinement
autoPROCdata reduction
PHASERphasing