7BRD

Crystal structure of Peptidyl-tRNA hydrolase from Klebsiella pneumoniae

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	295	0.2M Ammonium Sulfate 0.1M Sodium cacodylate 30% PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.203	α = 90
b = 72.372	β = 90
c = 77.415	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	IMAGE PLATE	RIGAKU RAXIS IV++		2019-12-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.54178

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	1.89	31.97	100	0.155	0.163	0.049	0.997	10.6	10.6		31852			22.06

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	1.97	99.6		0.127	0.89	0.271	0.827		10.3

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	2PTH	1.892	25.208	31852	1537	99.116	0.176	0.1738	0.2218	21.807

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]
-0.348			0.071		0.277

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.923
r_dihedral_angle_4_deg	16.704
r_dihedral_angle_3_deg	12.594
r_dihedral_angle_1_deg	6.721
r_lrange_it	5.84
r_lrange_other	5.839
r_scangle_it	2.928
r_scangle_other	2.927
r_mcangle_it	2.259
r_mcangle_other	2.259
r_scbond_it	1.972
r_scbond_other	1.971
r_angle_refined_deg	1.792
r_angle_other_deg	1.483
r_mcbond_it	1.462
r_mcbond_other	1.441
r_symmetry_nbd_refined	0.313
r_nbd_other	0.229
r_nbd_refined	0.217
r_symmetry_nbd_other	0.182
r_xyhbond_nbd_refined	0.178
r_symmetry_xyhbond_nbd_refined	0.167
r_nbtor_refined	0.165
r_ncsr_local_group_1	0.124
r_chiral_restr	0.094
r_symmetry_nbtor_other	0.083
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2877
Nucleic Acid Atoms
Solvent Atoms	298
Heterogen Atoms	120

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing