9VYL | pdb_00009vyl

Crystal structure of BdThsB1 with NAD


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5283.1510mg/ml protein, 160mM MgCl2, 100mM Tris pH7.5, 22.6% (w/v) PEG3350 (well) 1:1:0.2 protein/well/additive. the additive solution is 100mM Spermidine
Crystal Properties
Matthews coefficientSolvent content
2.3948.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.586α = 90
b = 43.574β = 90.031
c = 285.783γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2025-03-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 5C (4A)1PAL/PLS5C (4A)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)Rpim I (All)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
11.5395099.70.070.0380.99723.095.78159272
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.541.570.5180.290.7932.25

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 REPLACEMENTNONE1.53934.668159254783499.5440.1490.14720.14720.18280.182720.506
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]
-0.015-0.0030.0010.014
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it19.154
r_lrange_other17.49
r_dihedral_angle_6_deg16.079
r_dihedral_angle_3_deg12.121
r_scangle_it11.953
r_scangle_other11.952
r_dihedral_angle_2_deg10.675
r_mcangle_it8.771
r_mcangle_other8.771
r_scbond_it8.412
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it19.154
r_lrange_other17.49
r_dihedral_angle_6_deg16.079
r_dihedral_angle_3_deg12.121
r_scangle_it11.953
r_scangle_other11.952
r_dihedral_angle_2_deg10.675
r_mcangle_it8.771
r_mcangle_other8.771
r_scbond_it8.412
r_scbond_other8.412
r_mcbond_it6.09
r_mcbond_other6.088
r_dihedral_angle_1_deg5.448
r_rigid_bond_restr4.579
r_dihedral_angle_other_2_deg2.054
r_angle_refined_deg1.66
r_angle_other_deg1.098
r_chiral_restr_other1.006
r_nbd_refined0.241
r_symmetry_nbd_refined0.223
r_symmetry_nbd_other0.213
r_nbd_other0.191
r_nbtor_refined0.189
r_symmetry_xyhbond_nbd_refined0.183
r_xyhbond_nbd_refined0.152
r_metal_ion_refined0.119
r_chiral_restr0.083
r_symmetry_nbtor_other0.082
r_symmetry_xyhbond_nbd_other0.034
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_gen_planes_other0.005
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7328
Nucleic Acid Atoms
Solvent Atoms1010
Heterogen Atoms284

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing