8APT

Crystal Structure of H. influenzae TrmD in complex with Compound 13


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4YVH 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529120% PEG3350 0.1 M HEPES, pH 7.5 0.1 M potassium citrate tribasic
Crystal Properties
Matthews coefficientSolvent content
2.6553.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.671α = 90
b = 94.671β = 90
c = 177.958γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2020-09-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.847.3899.80.1570.1740.0750.99714.910.528700
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.841.1861.3570.6430.5597.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE4YVH1.847.3828698293199.8050.1630.16130.179418.697
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]
0.0020.0010.002-0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.577
r_dihedral_angle_3_deg14.019
r_dihedral_angle_4_deg11.995
r_lrange_it11.218
r_lrange_other10.667
r_dihedral_angle_1_deg6.534
r_scangle_it4.899
r_scangle_other4.897
r_scbond_it3.338
r_scbond_other3.319
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.577
r_dihedral_angle_3_deg14.019
r_dihedral_angle_4_deg11.995
r_lrange_it11.218
r_lrange_other10.667
r_dihedral_angle_1_deg6.534
r_scangle_it4.899
r_scangle_other4.897
r_scbond_it3.338
r_scbond_other3.319
r_mcangle_it2.931
r_mcangle_other2.931
r_mcbond_it2.158
r_mcbond_other2.147
r_angle_refined_deg1.847
r_angle_other_deg1.521
r_symmetry_xyhbond_nbd_refined0.412
r_xyhbond_nbd_refined0.33
r_nbd_other0.252
r_nbd_refined0.231
r_symmetry_nbd_other0.203
r_symmetry_nbd_refined0.189
r_nbtor_refined0.172
r_chiral_restr0.108
r_symmetry_xyhbond_nbd_other0.09
r_symmetry_nbtor_other0.087
r_bond_refined_d0.017
r_gen_planes_refined0.012
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1947
Nucleic Acid Atoms
Solvent Atoms416
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
StructureStudiodata collection
PHASERphasing