4KDT | pdb_00004kdt

Structure of an early native-like intermediate of beta2-microglobulin amyloidosis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2X89	pdb entry 2X89

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	0.1 M MES, 1.6 M MgSO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.66	66.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.79	α = 90
b = 96.79	β = 90
c = 167.79	γ = 90

Symmetry
Space Group	P 42 21 2

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 PILATUS 6M		2012-03-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97950	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.6	50	99.9		14.3	25281	25281

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.67	99.8		1.01	14.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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 2X89	2.6	48.43	25281	24016	1264	99.89	0.22847	0.22607	0.23	0.2737	0.27	RANDOM	58.836

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]
-0.84			-0.84		1.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.611
r_dihedral_angle_4_deg	19.742
r_dihedral_angle_3_deg	17.179
r_dihedral_angle_1_deg	7.371
r_angle_other_deg	3.657
r_mcangle_it	2.767
r_scbond_it	2.383
r_mcbond_it	1.622
r_mcbond_other	1.622
r_angle_refined_deg	1.55
r_chiral_restr	0.086
r_bond_refined_d	0.015
r_gen_planes_refined	0.009
r_gen_planes_other	0.009
r_bond_other_d
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3564
Nucleic Acid Atoms
Solvent Atoms	50
Heterogen Atoms	42

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling