2XMM | pdb_00002xmm

Visualising the Metal-binding Versatility of Copper Trafficking Sites: H61Y Atx1 side-to-side

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2XMJ	PDB ENTRY 2XMJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		25 % (W/V) PEG 8000, 200 MM SODIUM ACETATE AND 100 MM SODIUM CACODYLATE PH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.7	54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.63	α = 90
b = 41.4	β = 106.76
c = 55.58	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	CCD	ADSC CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03		Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.65	34.06	98	0.11	14.1	5.2		16218			17.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.65	1.74	95.7		0.29	4	5.3

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2XMJ	1.65	53.22	15398	786	97.75	0.16718	0.16544	0.17	0.20037	0.2	RANDOM	13.946

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]
1.19		-0.55	-0.43		-1.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.584
r_dihedral_angle_3_deg	10.895
r_dihedral_angle_4_deg	6.946
r_dihedral_angle_1_deg	5.45
r_scangle_it	4.35
r_scbond_it	2.515
r_mcangle_it	1.389
r_angle_refined_deg	1.225
r_angle_other_deg	0.837
r_mcbond_it	0.744
r_symmetry_vdw_refined	0.307
r_mcbond_other	0.226
r_nbd_refined	0.224
r_symmetry_vdw_other	0.198
r_nbd_other	0.177
r_nbtor_refined	0.165
r_xyhbond_nbd_refined	0.153
r_symmetry_hbond_refined	0.138
r_nbtor_other	0.084
r_chiral_restr	0.076
r_symmetry_metal_ion_refined	0.074
r_metal_ion_refined	0.073
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	901
Nucleic Acid Atoms
Solvent Atoms	190
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing