1Y46

T-To-T(High) quaternary transitions in human hemoglobin: betaW37Y deoxy low-salt (10 test sets)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Y0WPDB ENTRY 1Y0W

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1batch729810% PEG 6000, 10 mM potassium phosphate, 100 mM potassium chloride, 3 mM sodium dithionite, 10 mg/ml Hb, pH 7.0, batch, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.5752.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.2α = 90
b = 99.4β = 90
c = 66.1γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298AREA DETECTORSDMSGRAPHITE1996-07-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.225097.80.1115.66.431603
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.222.3989.60.2751.43.35691

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT and local R-freePDB ENTRY 1Y0W2.221028295313995.820.192090.186460.2426110 unique sets matched to pdb entry 1Y0W17.656
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]
0.230.22-0.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.97
r_dihedral_angle_1_deg3.606
r_scangle_it3.225
r_scbond_it1.955
r_angle_refined_deg1.782
r_mcangle_it1.233
r_angle_other_deg1.122
r_mcbond_it0.648
r_nbd_refined0.257
r_xyhbond_nbd_refined0.223
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.97
r_dihedral_angle_1_deg3.606
r_scangle_it3.225
r_scbond_it1.955
r_angle_refined_deg1.782
r_mcangle_it1.233
r_angle_other_deg1.122
r_mcbond_it0.648
r_nbd_refined0.257
r_xyhbond_nbd_refined0.223
r_nbd_other0.209
r_xyhbond_nbd_other0.199
r_symmetry_hbond_refined0.181
r_symmetry_vdw_other0.176
r_symmetry_vdw_refined0.112
r_chiral_restr0.087
r_bond_refined_d0.019
r_gen_planes_refined0.006
r_gen_planes_other0.006
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4382
Nucleic Acid Atoms
Solvent Atoms175
Heterogen Atoms172

Software

Software
Software NamePurpose
SDMSdata collection
SDMSdata reduction
X-PLORmodel building
REFMACrefinement
SDMSdata scaling
X-PLORphasing