8TI5 | pdb_00008ti5

Crystal structure of Tyr p 36.0101

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ACF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	0.1 M citric acid pH 3.5, 2 M ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.364	α = 90
b = 55.364	β = 90
c = 78.814	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		2022-02-22	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	1.15	40	95.3	0.06	0.06	0.063	0.02	0.995	34.8	9.7		47953		-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	1.15	1.17	57.8		0.304	0.304	0.349	0.164	0.919	2.5

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	1.15	30.462	43128	2044	85.794	0.15	0.1485	0.16	0.1706	0.18	15.857

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]
-0.175	-0.088		-0.175		0.568

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.243
r_dihedral_angle_2_deg	14.129
r_dihedral_angle_3_deg	12.597
r_dihedral_angle_1_deg	6.561
r_rigid_bond_restr	3.802
r_lrange_it	3.635
r_lrange_other	2.814
r_scangle_it	1.934
r_scangle_other	1.916
r_angle_refined_deg	1.698
r_mcangle_it	1.534
r_mcangle_other	1.533
r_scbond_it	1.457
r_scbond_other	1.446
r_mcbond_it	1.1
r_mcbond_other	1.098
r_angle_other_deg	0.695
r_nbd_other	0.244
r_nbd_refined	0.222
r_symmetry_nbd_refined	0.222
r_symmetry_nbd_other	0.21
r_xyhbond_nbd_refined	0.189
r_nbtor_refined	0.182
r_symmetry_xyhbond_nbd_refined	0.13
r_chiral_restr	0.092
r_symmetry_nbtor_other	0.087
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_gen_planes_other	0.005
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	995
Nucleic Acid Atoms
Solvent Atoms	186
Heterogen Atoms	20

Software

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