1YGD | pdb_00001ygd

T-To-T(High) quaternary transitions in human hemoglobin: betaW37E alpha zinc beta oxy (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	1Y4P	PDB ENTRY 1Y4P

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 13% PEG 6000, 10 MM POTASSIUM PHOSPHATE (PH 7.0), 100 MM POTASSIUM CHLORIDE. THE CRYSTAL WAS THEN EXPOSED TO AIR AT 298K AND DATA WAS COLLECTED AT 298K.

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.3	α = 90
b = 99.1	β = 90
c = 66.8	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	298	AREA DETECTOR	SDMS	GRAPHITE	1997-12-23	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	2.73	50	97.9	0.134	5	5.7		17254

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)
	2.73	2.94	90.5		0.301	1.5	4.3	3138

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 1Y4P	2.73	10	15089	1699	97.75	0.19752	0.18993	0.19	0.26603	0.26	10 SETS MATCHED TO PDB ENTRY 1Y4P	22.865

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]
-1.18			1.2		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.057
r_dihedral_angle_1_deg	2.483
r_scangle_it	1.907
r_angle_refined_deg	1.378
r_scbond_it	1.156
r_mcangle_it	0.9
r_mcbond_it	0.47
r_symmetry_vdw_refined	0.305
r_nbd_refined	0.264
r_xyhbond_nbd_refined	0.208
r_symmetry_hbond_refined	0.163
r_chiral_restr	0.079
r_metal_ion_refined	0.031
r_bond_refined_d	0.019
r_gen_planes_refined	0.003
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
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
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	175
Heterogen Atoms	176

Software

Software
Software Name	Purpose
SDMS	data collection
SDMS	data reduction
X-PLOR	model building
REFMAC	refinement
SDMS	data scaling
X-PLOR	phasing