1Y09

T-to-T(High) Quaternary Transitions in Human Hemoglobin: alphaN97A deoxy low-salt


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RQ3pdb entry 1RQ3

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
2.5752.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.26α = 90
b = 99.36β = 90
c = 65.91γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray277IMAGE PLATERIGAKU RAXIS IVosmic mirrors2004-05-05MSINGLE 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
12.255087.60.0588.22.72692826928
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)
2.252.4372.50.1464.71.74527

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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-free analysispdb entry 1RQ32.25102692823033263783.890.160560.155380.2062510 mutually exclusive test sets matched to pdb entry 1RQ332.639
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]
-0.231.87-1.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.91
r_scangle_it4.16
r_dihedral_angle_1_deg3.913
r_scbond_it2.593
r_angle_refined_deg1.956
r_mcangle_it1.706
r_angle_other_deg1.196
r_mcbond_it0.899
r_symmetry_vdw_other0.29
r_nbd_refined0.248
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.91
r_scangle_it4.16
r_dihedral_angle_1_deg3.913
r_scbond_it2.593
r_angle_refined_deg1.956
r_mcangle_it1.706
r_angle_other_deg1.196
r_mcbond_it0.899
r_symmetry_vdw_other0.29
r_nbd_refined0.248
r_xyhbond_nbd_refined0.208
r_symmetry_vdw_refined0.206
r_nbd_other0.205
r_symmetry_hbond_refined0.2
r_xyhbond_nbd_other0.148
r_chiral_restr0.101
r_bond_refined_d0.022
r_gen_planes_refined0.007
r_gen_planes_other0.006
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4374
Nucleic Acid Atoms
Solvent Atoms175
Heterogen Atoms172

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
MOSFLMdata reduction
CCP4data scaling
X-PLORphasing