8V5Y

Crystal structure of Tyr p 36.0101 in complex with a poly(L-proline) peptide

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	3.5	298	0.1 M lithium citrate pH 3.5, 2.0 M ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.15	42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.289	α = 90
b = 55.518	β = 121.179
c = 59.032	γ = 90

Symmetry
Space Group	C 1 2 1

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 EIGER X 16M		2023-10-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-2	0.979	NSLS-II	17-ID-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.05	40	91.4	0.075	0.075	0.082	0.033	0.989	16.6	5.4		13911

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.05	2.09	65.1		0.214	0.214	0.267	0.157	0.932	2.5	2.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.059	37.768	13909	695	91.057	0.171	0.1687	0.2153	21.047

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]
0.061		-0.092	0.223		-0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.06
r_dihedral_angle_3_deg	12.628
r_dihedral_angle_2_deg	7.516
r_dihedral_angle_1_deg	6.697
r_lrange_it	6.302
r_lrange_other	6.122
r_scangle_it	4.033
r_scangle_other	3.992
r_scbond_it	2.564
r_mcangle_other	2.49
r_mcangle_it	2.489
r_scbond_other	2.488
r_mcbond_it	1.575
r_mcbond_other	1.575
r_angle_refined_deg	1.483
r_angle_other_deg	0.497
r_nbd_other	0.235
r_nbd_refined	0.207
r_symmetry_nbd_other	0.207
r_symmetry_xyhbond_nbd_refined	0.2
r_symmetry_nbd_refined	0.189
r_nbtor_refined	0.174
r_xyhbond_nbd_refined	0.171
r_ncsr_local_group_1	0.151
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.069
r_chiral_restr_other	0.022
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2040
Nucleic Acid Atoms
Solvent Atoms	220
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing