8APU | pdb_00008apu

Crystal Structure of H. influenzae TrmD in complex with Compound 14

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
2.64	53.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.607	α = 90
b = 94.607	β = 90
c = 177.954	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	1.9	47.348	99.1	0.116	0.128	0.052	0.999	17.8	10.9		24197

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	1.9	1.94			1.33	1.463	0.601	0.726		10.8

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	1.9	47.348	24191	2453	98.783	0.176	0.1742	0.19	0.1933	0.2	27.299

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		0.008

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.348
r_dihedral_angle_3_deg	15.109
r_dihedral_angle_4_deg	12.305
r_lrange_it	7.877
r_lrange_other	7.876
r_dihedral_angle_1_deg	6.496
r_scangle_it	5.881
r_scangle_other	5.879
r_scbond_it	4.192
r_scbond_other	4.182
r_mcangle_it	4.169
r_mcangle_other	4.167
r_mcbond_it	2.983
r_mcbond_other	2.976
r_angle_refined_deg	1.821
r_angle_other_deg	1.489
r_xyhbond_nbd_refined	0.288
r_symmetry_xyhbond_nbd_refined	0.238
r_nbd_other	0.236
r_nbd_refined	0.216
r_symmetry_nbd_other	0.2
r_nbtor_refined	0.17
r_symmetry_nbd_refined	0.124
r_chiral_restr	0.101
r_symmetry_nbtor_other	0.087
r_symmetry_xyhbond_nbd_other	0.05
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	286
Heterogen Atoms	32

Software

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