1Y5J

T-To-T(High) quaternary transitions in human hemoglobin: betaH97A deoxy low-salt (1 test set)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Y0TPDB ENTRY 1Y0T

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
2.5451.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.1α = 90
b = 98.6β = 90
c = 65.9γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298AREA DETECTORSDMSGRAPHITE1994-11-08MSINGLE 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
12.035097.10.1017.911.64040340403
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)
2.032.1885.90.2871.95.27057

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1Y0T2.031023962039105315497.10.1810.245MATCHED TO PDB ENTRY 1Y0T24.51
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]
RMS Deviations
KeyRefinement Restraint Deviation
p_transverse_tor32.4
p_staggered_tor20.6
p_scangle_it7.163
p_scbond_it5.553
p_mcangle_it3.255
p_mcbond_it2.331
p_planar_tor2.2
p_xyhbond_nbd0.18
p_multtor_nbd0.171
p_singtor_nbd0.165
RMS Deviations
KeyRefinement Restraint Deviation
p_transverse_tor32.4
p_staggered_tor20.6
p_scangle_it7.163
p_scbond_it5.553
p_mcangle_it3.255
p_mcbond_it2.331
p_planar_tor2.2
p_xyhbond_nbd0.18
p_multtor_nbd0.171
p_singtor_nbd0.165
p_chiral_restr0.125
p_hb_or_metal_coord0.122
p_planar_d0.04
p_angle_d0.025
p_bond_d0.01
p_plane_restr0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4376
Nucleic Acid Atoms
Solvent Atoms194
Heterogen Atoms172

Software

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