5HY8 | pdb_00005hy8

Glycation restrains allosteric transition in hemoglobin: The molecular basis of oxidative stress under hyperglycemic conditions in diabetes

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 237.987	α = 90
b = 59.267	β = 125.36
c = 137.024	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	120	CCD	MAR CCD 165 mm		2003-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.954	SLS	X06SA

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	112.13	87	23.7	3.1		69814

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	2.3	3.36	55.1		0.386

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	1HHO	2.3	112.13	57698	3020	86.97	0.2053	0.2033	0.2583	0.2443	0.2868	RANDOM	109.574

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]
-0.62		-1.21	3.33		-0.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.443
r_dihedral_angle_4_deg	17.129
r_dihedral_angle_3_deg	15.779
r_dihedral_angle_1_deg	5.876
r_angle_other_deg	3.85
r_mcangle_it	2.871
r_angle_refined_deg	1.948
r_mcbond_it	1.806
r_mcbond_other	1.799
r_chiral_restr	0.142

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.443
r_dihedral_angle_4_deg	17.129
r_dihedral_angle_3_deg	15.779
r_dihedral_angle_1_deg	5.876
r_angle_other_deg	3.85
r_mcangle_it	2.871
r_angle_refined_deg	1.948
r_mcbond_it	1.806
r_mcbond_other	1.799
r_chiral_restr	0.142
r_gen_planes_other	0.039
r_bond_refined_d	0.019
r_gen_planes_refined	0.013
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10886
Nucleic Acid Atoms
Solvent Atoms	232
Heterogen Atoms	491

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.