6TUD | pdb_00006tud

Crystal structure of Y. pestis penicillin-binding protein 3

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6SYN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		296	1 uL of protein (in 20 mM Tris-HCl pH 7.5 150 mM NaCl and 2 mM carbenicillin) at 7 mg/ml and 0.2 uL of precipitant (0.2 M magnesium acetate, 6% gamma-PGA (Na+ form, LM) and 6% PEG8000) Crystals were then dehydrated by replacing 50% of the reservoir solution with 50% PEG10000

Crystal Properties
Matthews coefficient	Solvent content
3.47	65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.8	α = 90
b = 100.8	β = 90
c = 314.409	γ = 90

Symmetry
Space Group	P 41 21 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	PIXEL	DECTRIS PILATUS 6M-F		2018-01-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9196	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	3	29.64	99.9	0.2	0.071	0.997	9.1	10		33546			50.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3	3.15	100		1.099	0.518	0.941	1.4

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	6SYN	3	29.64	33459	1713	99.836	0.245	0.2439	0.25	0.2764	0.28	82.519

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]
7.716			7.716		-15.432

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.564
r_dihedral_angle_3_deg	16.545
r_dihedral_angle_4_deg	12.879
r_dihedral_angle_1_deg	5.288
r_lrange_it	4.756
r_lrange_other	4.756
r_mcangle_it	2.861
r_mcangle_other	2.861
r_scangle_it	2.069
r_scangle_other	2.069
r_mcbond_it	1.576
r_mcbond_other	1.573
r_angle_refined_deg	1.197
r_scbond_it	1.069
r_scbond_other	1.069
r_angle_other_deg	1.029
r_symmetry_xyhbond_nbd_refined	0.222
r_nbd_other	0.184
r_symmetry_nbd_refined	0.182
r_symmetry_nbd_other	0.172
r_nbd_refined	0.167
r_nbtor_refined	0.146
r_xyhbond_nbd_refined	0.134
r_symmetry_nbtor_other	0.073
r_chiral_restr	0.033
r_bond_refined_d	0.002
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7019
Nucleic Acid Atoms
Solvent Atoms	27
Heterogen Atoms

Software

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