6AFK | pdb_00006afk

Crystal structure of TrmD from Pseudomonas aeruginosa in complex with active-site inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5WYQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293.15	0.1M Tris-HCl at pH 8.6-8.8, 20%(v/v) MPD, 20%(w/v) PEG1000, 5%(w/v) PEG200

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.02	α = 90
b = 86.02	β = 90
c = 149.191	γ = 120

Symmetry
Space Group	P 32 2 1

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	ADSC QUANTUM 210r		2016-06-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX1	0.95370	Australian Synchrotron	MX1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.75	74.5	100	0.143	14	10.8		17233

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.75	2.88	100		1.202

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5WYQ	2.75	52.77	16300	893	99.97	0.18371	0.18012	0.19	0.24877	0.26	RANDOM	59.651

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]
0.46	0.23		0.46		-1.49

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.832
r_dihedral_angle_3_deg	21.13
r_dihedral_angle_4_deg	19.825
r_long_range_B_refined	11.424
r_long_range_B_other	11.41
r_scangle_other	6.972
r_mcangle_it	6.347
r_mcangle_other	6.345
r_dihedral_angle_1_deg	5.655
r_scbond_it	4.427
r_scbond_other	4.426
r_mcbond_it	4.143
r_mcbond_other	4.143
r_angle_refined_deg	1.047
r_angle_other_deg	0.831
r_chiral_restr	0.053
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3820
Nucleic Acid Atoms
Solvent Atoms	186
Heterogen Atoms	56

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing