3ATO | pdb_00003ato

Glycine ethyl ester shielding on the aromatic surfaces of lysozyme: Implication for suppression of protein aggregation

X-RAY DIFFRACTION

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Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
1.92	35.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.171	α = 90
b = 77.171	β = 90
c = 36.898	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	2010-12-08	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)	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	1.17	40	99.4				36120

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	1.17	1.21	98.5

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 (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	1.17	30.57	36120	1879	98.95	0.155	0.15397	0.1512	0.1748	0.1526	RANDOM	14.573

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]
0.01			0.01		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.08
r_dihedral_angle_4_deg	12.698
r_dihedral_angle_3_deg	12.149
r_sphericity_free	10.96
r_sphericity_bonded	7.499
r_dihedral_angle_1_deg	6.125
r_scangle_it	4.699
r_scbond_it	3.418
r_mcangle_it	2.847
r_mcbond_it	1.96
r_rigid_bond_restr	1.957
r_angle_refined_deg	1.584
r_symmetry_vdw_refined	0.352
r_nbtor_refined	0.307
r_nbd_refined	0.228
r_metal_ion_refined	0.145
r_xyhbond_nbd_refined	0.133
r_chiral_restr	0.109
r_symmetry_hbond_refined	0.106
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
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	116
Heterogen Atoms	32

Software

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