9EY6

Crystal structure of human tyrosinase-related protein 1 (TYRP1)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5M8L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	277	PEG 6000, zinc chloride, Tris-HCl pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
4.31	71.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.754	α = 90
b = 103.754	β = 90
c = 140.988	γ = 120

Symmetry
Space Group	P 32 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 PILATUS3 2M		2020-09-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.8731	ESRF	ID23-2

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	2.227	50	99.06	0.1136	0.1295	0.06149	0.994	6.55	4.4		81266			44.72

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.24	2.29	86.53		1.158	0.6229	0.46		4.1

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	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.228	44.967	42682	2108	98.043	0.172	0.1698	0.2127	RANDOM	52.36

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]
0.698	0.349		0.698		-2.265

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.198
r_dihedral_angle_3_deg	14.569
r_lrange_other	11.199
r_lrange_it	11.177
r_dihedral_angle_2_deg	9.925
r_scangle_it	9.837
r_scangle_other	9.835
r_mcangle_it	6.899
r_mcangle_other	6.898
r_scbond_it	6.783
r_scbond_other	6.783
r_dihedral_angle_1_deg	6.56
r_mcbond_it	4.791
r_mcbond_other	4.789
r_angle_refined_deg	1.868
r_angle_other_deg	0.662
r_symmetry_nbd_refined	0.375
r_symmetry_xyhbond_nbd_other	0.344
r_metal_ion_refined	0.287
r_nbd_other	0.219
r_nbd_refined	0.218
r_xyhbond_nbd_refined	0.218
r_symmetry_nbd_other	0.198
r_chiral_restr	0.186
r_nbtor_refined	0.182
r_symmetry_metal_ion_refined	0.118
r_symmetry_nbtor_other	0.115
r_symmetry_xyhbond_nbd_refined	0.08
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3571
Nucleic Acid Atoms
Solvent Atoms	182
Heterogen Atoms	279

Software

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