1Y5K

T-To-T(High) quaternary transitions in human hemoglobin: betaD99A 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
2.5952.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.46α = 90
b = 99.88β = 90
c = 66γ = 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
12.25080.30.0699.25.426819
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)
2.22.3835.10.2223.12.32292

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 1Y0W2.21022469249875.640.167830.161220.2265510 SETS MATCHED to PDB ENTRY 1Y0W29
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]
-0.432.53-2.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg19.082
r_scangle_it4.422
r_dihedral_angle_1_deg4.076
r_scbond_it2.712
r_angle_refined_deg2.056
r_mcangle_it1.745
r_angle_other_deg1.271
r_mcbond_it0.936
r_xyhbond_nbd_other0.27
r_nbd_refined0.264
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg19.082
r_scangle_it4.422
r_dihedral_angle_1_deg4.076
r_scbond_it2.712
r_angle_refined_deg2.056
r_mcangle_it1.745
r_angle_other_deg1.271
r_mcbond_it0.936
r_xyhbond_nbd_other0.27
r_nbd_refined0.264
r_xyhbond_nbd_refined0.242
r_symmetry_hbond_refined0.242
r_nbd_other0.216
r_symmetry_vdw_other0.214
r_symmetry_vdw_refined0.199
r_chiral_restr0.114
r_bond_refined_d0.023
r_gen_planes_refined0.008
r_gen_planes_other0.007
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4380
Nucleic Acid Atoms
Solvent Atoms175
Heterogen Atoms172

Software

Software
Software NamePurpose
CRYSTALdata collection
MOSFLMdata reduction
SCALAdata scaling
X-PLORmodel building
REFMACrefinement
CrystalCleardata reduction
CCP4data scaling
X-PLORphasing