1YH9 | pdb_00001yh9

T-to-T(High) quaternary transitions in human hemoglobin: HbA OXY (2MM IHP, 20% PEG) (10 test sets)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1RQ3	PDB ENTRY 1RQ3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				10% PEG 6000, 10 MM POTASSIUM PHOSPHATE, 100 MM POTASSIUM CHLORIDE, 3 MM SODIUM DITHIONITE, 10 MG/ML DEOXYHB, PH 7.0, BATCH, TEMPERATURE 298K, 1 ATM N2. EXPOSING DEOXY CRYSTAL TO LIGAND: A DEOXY CRYSTAL WAS SOAKED (UNDER 1 ATM NITROGEN) IN SUBSTITUTE MOTHER LIQUOR CONTAINING 20% PEG 6000, 10 MM POTASSIUM PHOSPHATE (PH 7.0), 100 MM POTASSIUM CHLORIDE, AND 2.2 MM IHP. THE IHP-STABILIZED CRYSTAL WAS THEN EXPOSED TO 1 ATM OF OXYGEN AT 177K AND DATA WAS COLLECTED AT 169K.

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.1	α = 90
b = 99.6	β = 90
c = 66.1	γ = 90

Symmetry
Space Group	P 21 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	169	IMAGE PLATE	RIGAKU RAXIS IV	OSMIC MIRRORS	2000-12-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

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	2.2	34.77	93.7	0.073	4.7	3.1		31525

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)
	2.2	2.37	87.7		0.266	3.3	2.7	8798

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	PDB ENTRY 1RQ3	2.2	10	26043	2971	88.36	0.19424	0.18956	0.2	0.23589	0.24	10 SETS MATCHED TO PDB ENTRY 1RQ3	30.531

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]
-0.41			1.4		-0.99

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.998
r_dihedral_angle_1_deg	3.099
r_scangle_it	2.303
r_scbond_it	1.401
r_angle_refined_deg	1.255
r_angle_other_deg	1.06
r_mcangle_it	0.99
r_mcbond_it	0.52
r_nbd_refined	0.239
r_nbd_other	0.197
r_symmetry_vdw_other	0.189
r_xyhbond_nbd_refined	0.183
r_symmetry_hbond_refined	0.173
r_symmetry_vdw_refined	0.113
r_chiral_restr	0.074
r_xyhbond_nbd_other	0.054
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_gen_planes_other	0.004
r_bond_other_d	0.001
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_nbtor_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4384
Nucleic Acid Atoms
Solvent Atoms	143
Heterogen Atoms	180

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
X-PLOR	model building
REFMAC	refinement
CCP4	data scaling
X-PLOR	phasing