1YDZ

T-To-T(High) quaternary transitions in human hemoglobin: alphaY140F oxy (2MM IHP, 20% PEG) (1 test set)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Y0CPDB ENTRY 1Y0C

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
2.5451.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.6α = 90
b = 98.6β = 90
c = 67.1γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray169IMAGE PLATERIGAKU RAXIS IVOSMIC MIRRORS2001-05-21MSINGLE 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
13.334.392.30.1145.82.89186
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)
3.33.5685.90.2412.82.71735

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 1Y0C3.31027990796871292.30.1270.307MATCHED TO PDB ENTRY 1Y0C20.66
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_tor31.6
p_staggered_tor25.2
p_scangle_it8.366
p_scbond_it5.589
p_mcangle_it3.559
p_planar_tor2.6
p_mcbond_it2.156
p_xyhbond_nbd0.218
p_multtor_nbd0.208
p_singtor_nbd0.179
RMS Deviations
KeyRefinement Restraint Deviation
p_transverse_tor31.6
p_staggered_tor25.2
p_scangle_it8.366
p_scbond_it5.589
p_mcangle_it3.559
p_planar_tor2.6
p_mcbond_it2.156
p_xyhbond_nbd0.218
p_multtor_nbd0.208
p_singtor_nbd0.179
p_hb_or_metal_coord0.17
p_chiral_restr0.148
p_planar_d0.043
p_angle_d0.027
p_bond_d0.01
p_plane_restr0.01
p_angle_deg
p_xhyhbond_nbd
p_orthonormal_tor
p_special_tor
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4378
Nucleic Acid Atoms
Solvent Atoms192
Heterogen Atoms180

Software

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