8APT | pdb_00008apt

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4YVH

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
2.65	53.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.671	α = 90
b = 94.671	β = 90
c = 177.958	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	1.8	47.38	99.8	0.157	0.174	0.075	0.997	14.9	10.5		28700

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	1.8	1.84			1.186	1.357	0.643	0.559		7.3

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4YVH	1.8	47.38	28698	2931	99.805	0.163	0.1613	0.18	0.1794	0.19	18.697

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]
0.002	0.001		0.002		-0.006

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.577
r_dihedral_angle_3_deg	14.019
r_dihedral_angle_4_deg	11.995
r_lrange_it	11.218
r_lrange_other	10.667
r_dihedral_angle_1_deg	6.534
r_scangle_it	4.899
r_scangle_other	4.897
r_scbond_it	3.338
r_scbond_other	3.319
r_mcangle_it	2.931
r_mcangle_other	2.931
r_mcbond_it	2.158
r_mcbond_other	2.147
r_angle_refined_deg	1.847
r_angle_other_deg	1.521
r_symmetry_xyhbond_nbd_refined	0.412
r_xyhbond_nbd_refined	0.33
r_nbd_other	0.252
r_nbd_refined	0.231
r_symmetry_nbd_other	0.203
r_symmetry_nbd_refined	0.189
r_nbtor_refined	0.172
r_chiral_restr	0.108
r_symmetry_xyhbond_nbd_other	0.09
r_symmetry_nbtor_other	0.087
r_bond_refined_d	0.017
r_gen_planes_refined	0.012
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1947
Nucleic Acid Atoms
Solvent Atoms	416
Heterogen Atoms	32

Software

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