1Y4P

T-To-T(high) quaternary transitions in human hemoglobin: betaW37E deoxy low-salt (10 test sets)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Y0WPDB ENTRY 1Y0W

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
2.5651.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.7α = 90
b = 99.1β = 90
c = 66.3γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298AREA DETECTORSDMSGRAPHITE1995-08-25MSINGLE 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
11.985096.70.0798.56.24334043340
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)
1.982.1484.20.2761.43.17440

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 REPLACEMENTTHROUGHOUT and local R-freePDB ENTRY 1Y0W1.981038599429295.980.19580.191850.2313210 sets matched to PDB ENTRY 1Y0W25.22
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]
-0.181.18-1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.303
r_scangle_it3.868
r_dihedral_angle_1_deg3.624
r_scbond_it2.397
r_angle_refined_deg1.738
r_mcangle_it1.5
r_angle_other_deg1.154
r_mcbond_it0.783
r_nbd_refined0.239
r_xyhbond_nbd_refined0.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.303
r_scangle_it3.868
r_dihedral_angle_1_deg3.624
r_scbond_it2.397
r_angle_refined_deg1.738
r_mcangle_it1.5
r_angle_other_deg1.154
r_mcbond_it0.783
r_nbd_refined0.239
r_xyhbond_nbd_refined0.21
r_symmetry_vdw_other0.201
r_nbd_other0.2
r_symmetry_vdw_refined0.146
r_symmetry_hbond_refined0.142
r_xyhbond_nbd_other0.14
r_chiral_restr0.093
r_bond_refined_d0.018
r_gen_planes_refined0.007
r_gen_planes_other0.006
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4376
Nucleic Acid Atoms
Solvent Atoms175
Heterogen Atoms172

Software

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