1S69

The X-ray structure of the cyanobacteria Synechocystis hemoglobin "cyanoglobin" with cyanide ligand


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DLYPDB entry 1dly

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62771.5M sodium citrate, 0.2M ammonium citrate, 20% sucrose, 3% dioxane, 25mM sodium cyanide, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.9768.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.06α = 90
b = 84.06β = 90
c = 64.62γ = 90
Symmetry
Space GroupI 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2002-10-01MSINGLE WAVELENGTH
21x-ray100IMAGE PLATERIGAKU RAXIS IV2002-10-02MSINGLE WAVELENGTH
1,21
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418
2ROTATING ANODERIGAKU1.5418

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
1,21.6832.4975.20.05515.34.923795033
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)
1,21.681.7450.3432.11.02254

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1dly1.6832.53337837105380.460.199210.19270.192360.19921RANDOM28.241
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]
-0.38-0.380.75
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it5.658
r_dihedral_angle_1_deg5.294
r_scbond_it3.442
r_mcangle_it1.927
r_angle_refined_deg1.809
r_mcbond_it1.019
r_nbd_refined0.229
r_symmetry_hbond_refined0.217
r_xyhbond_nbd_refined0.197
r_symmetry_vdw_refined0.134
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it5.658
r_dihedral_angle_1_deg5.294
r_scbond_it3.442
r_mcangle_it1.927
r_angle_refined_deg1.809
r_mcbond_it1.019
r_nbd_refined0.229
r_symmetry_hbond_refined0.217
r_xyhbond_nbd_refined0.197
r_symmetry_vdw_refined0.134
r_chiral_restr0.121
r_bond_refined_d0.023
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms969
Nucleic Acid Atoms
Solvent Atoms148
Heterogen Atoms58

Software

Software
Software NamePurpose
REFMACrefinement
CRYSTALdata reduction
d*TREKdata scaling
CNSphasing