1YGF

T-to-T(high) quaternary transitions in human hemoglobin: betaH97A oxy (2MM IHP, 20% PEG) (1 test set)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Y5JPDB ENTRY 1Y5J

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 20% PEG 6000, 10 MM POTASSIUM PHOSPHATE (PH 7.0), 100 MM POTASSIUM CHLORIDE, AND 2.2 MM IHP. THE IHP-STABILIZED CRYSTAL WAS THEN EXPOSED TO 1 ATM OF OXYGEN AT 177K AND DATA WAS COLLECTED AT 169K.
Crystal Properties
Matthews coefficientSolvent content
2.5351.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.5α = 90
b = 98.3β = 90
c = 66.1γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray169IMAGE PLATERIGAKU RAXIS IVOSMIC MIRRORS2001-09-18MSINGLE 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
12.730.5790.20.0838.52.616077
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)
2.72.9281.60.24132.42951

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 1Y5J2.71011976296185.510.184670.163770.27039MATCHED TO PDB ENTRY 1Y5J34.392
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]
0.96-0.46-0.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg21.479
r_dihedral_angle_1_deg3.638
r_scangle_it2.553
r_angle_refined_deg1.73
r_scbond_it1.531
r_mcangle_it1.245
r_angle_other_deg1.131
r_mcbond_it0.657
r_symmetry_hbond_refined0.345
r_xyhbond_nbd_refined0.278
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg21.479
r_dihedral_angle_1_deg3.638
r_scangle_it2.553
r_angle_refined_deg1.73
r_scbond_it1.531
r_mcangle_it1.245
r_angle_other_deg1.131
r_mcbond_it0.657
r_symmetry_hbond_refined0.345
r_xyhbond_nbd_refined0.278
r_nbd_refined0.273
r_xyhbond_nbd_other0.251
r_symmetry_vdw_refined0.25
r_symmetry_vdw_other0.242
r_nbd_other0.229
r_chiral_restr0.085
r_bond_refined_d0.026
r_gen_planes_refined0.005
r_gen_planes_other0.004
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 Atoms4376
Nucleic Acid Atoms
Solvent Atoms192
Heterogen Atoms180

Software

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