1YEQ

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Y46PDB ENTRY 1Y46

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
110% 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 coefficientSolvent content
2.5852.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.2α = 90
b = 99.6β = 90
c = 67γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298AREA DETECTORSDMSGRAPHITE1996-10-02MSINGLE 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
12.755098.90.1715.55.317171
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)
2.752.9694.90.3011.53.93230

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1Y462.751014988169998.730.204280.196470.2743410 SETS MATCHED TO PDB ENTRY 1Y4622.25
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]
0.440.83-1.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg18.338
r_dihedral_angle_1_deg2.664
r_scangle_it2.004
r_angle_refined_deg1.341
r_scbond_it1.177
r_mcangle_it0.958
r_mcbond_it0.497
r_symmetry_hbond_refined0.304
r_nbd_refined0.275
r_symmetry_vdw_refined0.254
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg18.338
r_dihedral_angle_1_deg2.664
r_scangle_it2.004
r_angle_refined_deg1.341
r_scbond_it1.177
r_mcangle_it0.958
r_mcbond_it0.497
r_symmetry_hbond_refined0.304
r_nbd_refined0.275
r_symmetry_vdw_refined0.254
r_xyhbond_nbd_refined0.23
r_chiral_restr0.083
r_bond_refined_d0.027
r_gen_planes_refined0.003
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_refined
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 AtomsNumber
Protein Atoms4382
Nucleic Acid Atoms
Solvent Atoms134
Heterogen Atoms180

Software

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