1YGF | pdb_00001ygf

T-to-T(high) quaternary transitions in human hemoglobin: betaH97A oxy (2MM IHP, 20% PEG) (1 test set)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Y5J	PDB ENTRY 1Y5J

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
2.53	51.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.5	α = 90
b = 98.3	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	2001-09-18	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	2.7	30.57	90.2	0.083	8.5	2.6		16077

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)
	2.7	2.92	81.6		0.241	3	2.4	2951

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 1Y5J	2.7	10	11976	2961	85.51	0.18467	0.16377	0.19	0.27039	0.19	MATCHED TO PDB ENTRY 1Y5J	34.392

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]
0.96			-0.46		-0.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	21.479
r_dihedral_angle_1_deg	3.638
r_scangle_it	2.553
r_angle_refined_deg	1.73
r_scbond_it	1.531
r_mcangle_it	1.245
r_angle_other_deg	1.131
r_mcbond_it	0.657
r_symmetry_hbond_refined	0.345
r_xyhbond_nbd_refined	0.278
r_nbd_refined	0.273
r_xyhbond_nbd_other	0.251
r_symmetry_vdw_refined	0.25
r_symmetry_vdw_other	0.242
r_nbd_other	0.229
r_chiral_restr	0.085
r_bond_refined_d	0.026
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	4376
Nucleic Acid Atoms
Solvent Atoms	192
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