7CSN

Crystal structure of peptidyl-tRNA hydrolase from Acinetobacter baumannii at 1.00 A resolution

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, 20% Glycerol

Crystal Properties
Matthews coefficient	Solvent content
2	40

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34	α = 90
b = 66.25	β = 90
c = 76.23	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	PIXEL	PSI PILATUS 6M		2018-08-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.9720	ESRF	ID23-1

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	1	33.15	96.65	0.09	0.04	0.996	11.1	9.5		90567

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	1	1.02	98.8		0.79	0.42	0.74	2.4	8.5

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	FREE R-VALUE	6j93	1	33.147	89426	4520	95.406	0.145	0.1448	0.1569	15.225

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]
-0.122			0.2		-0.078

RMS Deviations
Key	Refinement Restraint Deviation
r_rigid_bond_restr	39.083
r_dihedral_angle_2_deg	34.865
r_dihedral_angle_4_deg	15.941
r_scbond_it	14.984
r_scbond_other	14.984
r_lrange_other	14.698
r_lrange_it	14.603
r_scangle_it	13.717
r_scangle_other	13.716
r_dihedral_angle_3_deg	12.552
r_mcbond_other	12.249
r_mcbond_it	12.242
r_mcangle_it	10.896
r_mcangle_other	10.892
r_dihedral_angle_1_deg	6.564
r_angle_refined_deg	2.514
r_angle_other_deg	1.794
r_symmetry_nbd_refined	0.301
r_xyhbond_nbd_refined	0.246
r_nbd_refined	0.242
r_nbd_other	0.239
r_symmetry_xyhbond_nbd_other	0.234
r_symmetry_nbd_other	0.208
r_symmetry_xyhbond_nbd_refined	0.187
r_nbtor_refined	0.183
r_chiral_restr	0.158
r_symmetry_nbtor_other	0.093
r_bond_refined_d	0.026
r_gen_planes_refined	0.013
r_bond_other_d	0.01
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1496
Nucleic Acid Atoms
Solvent Atoms	239
Heterogen Atoms

Software

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