1YHR

T-To-T(High) quaternary transitions in human hemoglobin: HbA OXY (10.0MM IHP, 20% PEG) (10 test sets)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RQ3PDB ENTRY 1RQ3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1729810% PEG 6000, 10 MM POTASSIUM PHOSPHATE, 100 MM POTASSIUM CHLORIDE, 3 MM SODIUM DITHIONITE, 10 MG/ML DEOXYHB, 1 ATM N2, pH 7.0, batch, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.5150.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.2α = 90
b = 98.4β = 90
c = 66.5γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray169IMAGE PLATERIGAKU RAXIS IVOSMIC MIRRORS2001-09-26MSINGLE 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
12.630.42994.70.0937.33.218673
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)
2.62.79890.2083.333549

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 1RQ32.61015836179290.690.184560.17490.2695510 SETS MATCHED TO PDB ENTRY 1RQ323.361
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]
0.2-0.09-0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg20.275
r_dihedral_angle_1_deg3.817
r_scangle_it3.562
r_scbond_it2.223
r_angle_refined_deg1.882
r_mcangle_it1.721
r_angle_other_deg1.17
r_mcbond_it0.928
r_symmetry_hbond_refined0.287
r_nbd_refined0.277
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg20.275
r_dihedral_angle_1_deg3.817
r_scangle_it3.562
r_scbond_it2.223
r_angle_refined_deg1.882
r_mcangle_it1.721
r_angle_other_deg1.17
r_mcbond_it0.928
r_symmetry_hbond_refined0.287
r_nbd_refined0.277
r_xyhbond_nbd_refined0.242
r_symmetry_vdw_other0.231
r_nbd_other0.226
r_symmetry_vdw_refined0.132
r_xyhbond_nbd_other0.096
r_chiral_restr0.095
r_bond_refined_d0.021
r_gen_planes_refined0.006
r_gen_planes_other0.005
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 Atoms4384
Nucleic Acid Atoms
Solvent Atoms153
Heterogen Atoms180

Software

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