2W6V

Structure of Human deoxy Hemoglobin A in complex with Xenon


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4HHBPDB ENTRY 4HHB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.53.2M (NH4)2SO4, 0.1M (NH4)H2PO4, 0.3M (NH4)2HPO4, PH 6.5, 0.2% DITHIONITE.
Crystal Properties
Matthews coefficientSolvent content
2.1342.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.645α = 90
b = 82.328β = 99.79
c = 53.552γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2000-05-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7AEMBL/DESY, HAMBURGBW7A

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
11.86198.80.0419.54.349841221.85
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)
11.791.9497.20.242.54.2

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 4HHB1.822.947136250299.70.1650.1620.216RANDOM20.57
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]
-0.030.010.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.898
r_dihedral_angle_3_deg14.696
r_dihedral_angle_4_deg14.502
r_dihedral_angle_1_deg9.954
r_scangle_it3.132
r_scbond_it2.122
r_angle_refined_deg1.624
r_mcangle_it1.193
r_mcbond_it0.739
r_nbtor_refined0.295
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.898
r_dihedral_angle_3_deg14.696
r_dihedral_angle_4_deg14.502
r_dihedral_angle_1_deg9.954
r_scangle_it3.132
r_scbond_it2.122
r_angle_refined_deg1.624
r_mcangle_it1.193
r_mcbond_it0.739
r_nbtor_refined0.295
r_nbd_refined0.222
r_symmetry_hbond_refined0.211
r_symmetry_vdw_refined0.194
r_xyhbond_nbd_refined0.181
r_chiral_restr0.1
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_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 Atoms576
Heterogen Atoms240

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALAdata scaling
MOLREPphasing