6LSO

Crystal structure of a dimeric inhibited of peptidyl tRNA hydrolase at 1.76A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	100mM HEPES, 20% PEG 1500

Crystal Properties
Matthews coefficient	Solvent content
2.51	51.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.56	α = 90
b = 98.33	β = 90
c = 123.93	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		2019-12-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	RRCAT INDUS-2 BEAMLINE PX-BL21	0.97	RRCAT INDUS-2	PX-BL21

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	1.76	45.74	98	0.13	0.14	0.058	0.991	8.4	6.2		42085

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	1.76	1.8	95		0.47	0.51	0.2	0.84	2.9	5.9

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	5YN4	1.76	45.74	42085	2063	98.002	0.184	0.1826	0.2184	14.094

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]
0.07			-0.577		0.507

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.382
r_dihedral_angle_3_deg	13.923
r_dihedral_angle_4_deg	13.746
r_dihedral_angle_1_deg	6.359
r_lrange_it	6.265
r_lrange_other	5.945
r_scangle_it	3.421
r_scangle_other	3.421
r_mcangle_it	2.43
r_mcangle_other	2.43
r_scbond_it	2.179
r_scbond_other	2.178
r_angle_refined_deg	1.617
r_mcbond_other	1.486
r_mcbond_it	1.485
r_angle_other_deg	1.482
r_symmetry_nbd_refined	0.314
r_symmetry_xyhbond_nbd_other	0.285
r_nbd_other	0.263
r_xyhbond_nbd_refined	0.238
r_nbd_refined	0.217
r_symmetry_nbd_other	0.193
r_symmetry_xyhbond_nbd_refined	0.187
r_nbtor_refined	0.162
r_chiral_restr	0.086
r_symmetry_nbtor_other	0.083
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2952
Nucleic Acid Atoms
Solvent Atoms	490
Heterogen Atoms

Software

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