1PY4 | pdb_00001py4

Beta2 microglobulin mutant H31Y displays hints for amyloid formations

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	300	PEG 4K 31%, glycerol 25%, ammonium acetate 0.2 M, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 300K

Crystal Properties
Matthews coefficient	Solvent content
3.88	68.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.195	α = 90
b = 150.166	β = 90
c = 93.671	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100					M	SINGLE WAVELENGTH
2	1	100

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 5.2R	0.927	ELETTRA	5.2R
2	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.939	ESRF	ID14-4

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.9	30	99.9	0.069	19.8		18871	16354

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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 1LDS	2.9	10	3	16354	15528	826	100	0.24084	0.23961	0.25	0.31308	0.34	RANDOM	57.002

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]
-1.33			4.75		-3.42

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	18.857
r_scbond_it	16.473
r_mcangle_it	16.232
r_mcbond_it	14.297
r_dihedral_angle_1_deg	10.376
r_angle_refined_deg	1.631
r_angle_other_deg	0.925
r_symmetry_hbond_refined	0.53
r_symmetry_vdw_other	0.412
r_nbd_refined	0.372
r_nbd_other	0.363
r_xyhbond_nbd_refined	0.318
r_symmetry_vdw_refined	0.276
r_chiral_restr	0.2
r_nbtor_other	0.106
r_bond_refined_d	0.014
r_gen_planes_refined	0.011
r_gen_planes_other	0.005
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_xyhbond_nbd_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3356
Nucleic Acid Atoms
Solvent Atoms	30
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
AMoRE	phasing