1YEO

T-To-T(High) quaternary transitions in human hemoglobin: betaW37A OXY (10 test sets)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Y4FPDB ENTRY 1Y4F

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
2.5651.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.89α = 90
b = 98.92β = 90
c = 66.83γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298AREA DETECTORSDMSGRAPHITE1995-12-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU200

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
12.225097.30.0769.37.631225
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)
2.222.3987.10.2222.13.3

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 1Y4F2.221027710306397.130.184660.180.22810 SETS MATCHED TO PDB ENTRY 1Y4F25.61
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]
-0.391.03-0.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg19.013
r_scangle_it3.444
r_dihedral_angle_1_deg3.343
r_scbond_it2.111
r_angle_refined_deg1.467
r_mcangle_it1.423
r_angle_other_deg1.096
r_mcbond_it0.734
r_symmetry_vdw_other0.252
r_nbd_refined0.248
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg19.013
r_scangle_it3.444
r_dihedral_angle_1_deg3.343
r_scbond_it2.111
r_angle_refined_deg1.467
r_mcangle_it1.423
r_angle_other_deg1.096
r_mcbond_it0.734
r_symmetry_vdw_other0.252
r_nbd_refined0.248
r_xyhbond_nbd_refined0.226
r_symmetry_vdw_refined0.211
r_symmetry_hbond_refined0.209
r_nbd_other0.205
r_xyhbond_nbd_other0.148
r_chiral_restr0.083
r_bond_refined_d0.026
r_nbtor_other0.021
r_gen_planes_refined0.006
r_gen_planes_other0.005
r_bond_other_d
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_nbtor_refined
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 AtomsNumber
Protein Atoms4396
Nucleic Acid Atoms
Solvent Atoms122
Heterogen Atoms180

Software

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