8APV

Crystal Structure of H. influenzae TrmD in complex with Compound 27

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291	20% PEG3350 0.1 M HEPES, pH 7.5 0.1 M potassium citrate tribasic

Crystal Properties
Matthews coefficient	Solvent content
2.64	53.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.63	α = 90
b = 94.63	β = 90
c = 178.015	γ = 120

Symmetry
Space Group	H 3 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	RIGAKU SATURN 944+		2020-09-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.4	47.36	100	0.17	0.199	0.102	0.994	11.6	6.9		12287

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)	Redundancy	Number Unique Reflections (All)
1	2.4	2.49			0.929	1.124	0.624	0.696		5.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4YVH	2.4	47.36	12287	588	99.886	0.181	0.1777	0.2526	29.48

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]
0.104	0.052		0.104		-0.339

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.4
r_dihedral_angle_3_deg	17.295
r_dihedral_angle_4_deg	16.031
r_lrange_it	7.639
r_lrange_other	7.634
r_dihedral_angle_1_deg	7.431
r_scangle_it	5.864
r_scangle_other	5.862
r_mcangle_other	5.144
r_mcangle_it	5.143
r_scbond_it	3.91
r_scbond_other	3.908
r_mcbond_it	3.479
r_mcbond_other	3.471
r_angle_refined_deg	1.898
r_angle_other_deg	1.392
r_symmetry_xyhbond_nbd_refined	0.445
r_nbd_other	0.219
r_nbd_refined	0.216
r_symmetry_nbd_other	0.186
r_xyhbond_nbd_refined	0.177
r_nbtor_refined	0.173
r_symmetry_nbd_refined	0.12
r_chiral_restr	0.091
r_symmetry_nbtor_other	0.084
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1947
Nucleic Acid Atoms
Solvent Atoms	94
Heterogen Atoms	34

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
StructureStudio	data collection
PHASER	phasing