8TI6 | pdb_00008ti6

Crystal structure of Tyr p 36.0101

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8TI5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	0.1 M citric acid pH 4.0, 0.8 M ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.974	α = 90
b = 54.974	β = 90
c = 79.315	γ = 120

Symmetry
Space Group	P 31 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		2022-07-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0000	APS	22-ID

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	1.42	40	96.8	0.057	0.057	0.06	0.018	1	38.9	10		25963		-3

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	1.42	1.44	72.7		0.309	0.309	0.358	0.171	0.889	2.1	3.7

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.42	30.49	25922	1219	96.782	0.134	0.1331	0.14	0.154	0.16	15.173

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]
0.157	0.079		0.157		-0.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	19.674
r_dihedral_angle_6_deg	15.24
r_dihedral_angle_3_deg	13.685
r_dihedral_angle_1_deg	6.533
r_rigid_bond_restr	3.732
r_lrange_other	2.452
r_lrange_it	2.436
r_scangle_it	1.707
r_scangle_other	1.706
r_angle_refined_deg	1.63
r_mcangle_other	1.427
r_mcangle_it	1.422
r_scbond_it	1.273
r_scbond_other	1.271
r_mcbond_it	0.985
r_mcbond_other	0.98
r_angle_other_deg	0.65
r_nbd_other	0.293
r_chiral_restr_other	0.262
r_nbd_refined	0.217
r_symmetry_nbd_other	0.205
r_nbtor_refined	0.176
r_symmetry_xyhbond_nbd_refined	0.168
r_symmetry_nbd_refined	0.167
r_xyhbond_nbd_refined	0.152
r_chiral_restr	0.091
r_symmetry_nbtor_other	0.085
r_symmetry_xyhbond_nbd_other	0.056
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_gen_planes_other	0.004
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	994
Nucleic Acid Atoms
Solvent Atoms	110
Heterogen Atoms	5

Software

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