6KL8

Crystal structure of Piptidyl t-RNA hydrolase from Acinetobacter baumannii with bound NaCl at the substrate binding site

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	12% PEG 1500, 0.1M HEPES, pH 7.5, 15% Glycerol

Crystal Properties
Matthews coefficient	Solvent content
2	38.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 33.961	α = 90
b = 66.099	β = 90
c = 75.825	γ = 90

Symmetry
Space Group	P 21 21 21

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	MARMOSAIC 225 mm CCD		2019-07-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	RRCAT INDUS-2 BEAMLINE PX-BL21	0.9795	RRCAT INDUS-2	PX-BL21

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	1.94	31.01	94.03	0.043	0.996	26.18	2.89		12479

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.94	2.05	91.1		0.049	0.996	21.11	2.72

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	THROUGHOUT	6J93	1.94	31.01	11218	1261	94.025	0.131	0.1268	0.1638	13.263

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]
-0.037			0.024		0.013

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.05
r_dihedral_angle_4_deg	19.24
r_dihedral_angle_3_deg	14.009
r_dihedral_angle_1_deg	6.623
r_lrange_it	6.136
r_lrange_other	6.134
r_scangle_it	3.678
r_scangle_other	3.676
r_mcangle_other	2.438
r_mcangle_it	2.437
r_scbond_it	2.319
r_scbond_other	2.318
r_angle_refined_deg	1.661
r_mcbond_it	1.513
r_mcbond_other	1.502
r_angle_other_deg	1.457
r_nbd_other	0.283
r_symmetry_xyhbond_nbd_other	0.214
r_symmetry_nbd_refined	0.213
r_nbd_refined	0.21
r_symmetry_nbd_other	0.201
r_xyhbond_nbd_refined	0.193
r_symmetry_xyhbond_nbd_refined	0.187
r_nbtor_refined	0.161
r_chiral_restr	0.085
r_symmetry_nbtor_other	0.085
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1496
Nucleic Acid Atoms
Solvent Atoms	187
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing