1YEV

T-To-T(High) quaternary transitions in human hemoglobin: betaW37E OXY (10 test sets)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Y4PPDB ENTRY 1Y4P

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
2.5852.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.07α = 90
b = 99.28β = 90
c = 67.02γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298AREA DETECTORSDMSGRAPHITE1998-09-27MSINGLE 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
12.115097.60.0839.26.936695
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)
2.112.2788.50.2731.63.36536

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 1Y4P2.111032553362497.230.198710.193940.2419310 SETS MATCHED TO PDB ENTRY 1Y4P27.925
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]
-0.981.58-0.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg19.22
r_scangle_it4.152
r_dihedral_angle_1_deg3.832
r_scbond_it2.63
r_angle_refined_deg1.707
r_mcangle_it1.657
r_angle_other_deg1.195
r_mcbond_it0.887
r_nbd_refined0.258
r_symmetry_hbond_refined0.242
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg19.22
r_scangle_it4.152
r_dihedral_angle_1_deg3.832
r_scbond_it2.63
r_angle_refined_deg1.707
r_mcangle_it1.657
r_angle_other_deg1.195
r_mcbond_it0.887
r_nbd_refined0.258
r_symmetry_hbond_refined0.242
r_symmetry_vdw_other0.229
r_xyhbond_nbd_refined0.215
r_nbd_other0.212
r_xyhbond_nbd_other0.204
r_symmetry_vdw_refined0.129
r_chiral_restr0.099
r_bond_refined_d0.03
r_gen_planes_refined0.008
r_gen_planes_other0.007
r_bond_other_d0.001
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 AtomsNumber
Protein Atoms4331
Nucleic Acid Atoms
Solvent Atoms115
Heterogen Atoms180

Software

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