5E29

Crystal Structure of Deoxygenated Hemoglobin in Complex with an Allosteric Effector and Nitric Oxide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2DN2PDB entry 2DN2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIQUID DIFFUSION6.52950.2 M sodium acetate trihydrate, 0.1 M sodium cacodylate trihydrate, pH 6.5, 30% w/v PEG8000, anaerobic conditions
Crystal Properties
Matthews coefficientSolvent content
2.4950.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.878α = 90
b = 98.419β = 90
c = 65.444γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2013-04-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODECu FINE FOCUS1.54

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
11.8529.5498.20.08412.35.535361352628
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)
11.851.9294.30.3134.54

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 2DN21.8529.5452628266998.10.2050.1980.253RANDOM25.9
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]
0.982.26-3.24
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d18.3
c_angle_deg1.4
c_improper_angle_d1.2
c_bond_d0.01
c_mcbond_it
c_mcangle_it
c_scbond_it
c_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4370
Nucleic Acid Atoms
Solvent Atoms973
Heterogen Atoms270

Software

Software
Software NamePurpose
d*TREKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
d*TREKdata reduction
PHENIXphasing