3AJN

Structural basis of glycine amide on suppression of protein aggregation by high resolution X-ray analysis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	193L	PDB ENTRY 193L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	Batch	4.5	293	0.05M sodium acetate, 1.0M glycine amide, pH 4.5, Batch, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.51	α = 90
b = 78.51	β = 90
c = 36.962	γ = 90

Symmetry
Space Group	P 43 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	IMAGE PLATE	RIGAKU RAXIS V	mirrors	2010-05-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL32B2	1.000	SPring-8	BL32B2

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	1.05	50		0.039		6.8		102269

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)
	1.05	1.09	94		0.308	5.5	3.5

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 193L	1.05	30	51208	2738	99.27	0.14674	0.1459	0.16306	RANDOM	14.174

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]
-0.02			-0.02		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.816
r_dihedral_angle_4_deg	18.176
r_dihedral_angle_3_deg	12.437
r_sphericity_free	11.498
r_sphericity_bonded	7.253
r_dihedral_angle_1_deg	6.228
r_scangle_it	5.099
r_scbond_it	3.819
r_mcangle_it	3.21
r_mcbond_it	2.234
r_rigid_bond_restr	2.129
r_angle_refined_deg	2.006
r_nbtor_refined	0.305
r_symmetry_hbond_refined	0.267
r_nbd_refined	0.261
r_symmetry_vdw_refined	0.175
r_metal_ion_refined	0.17
r_xyhbond_nbd_refined	0.15
r_chiral_restr	0.132
r_bond_refined_d	0.02
r_gen_planes_refined	0.012
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1001
Nucleic Acid Atoms
Solvent Atoms	159
Heterogen Atoms	23

Software

Software
Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling