2HZ3

The x-ray crystal structure of ferrous Synechocystis hemoglobin H117A mutant with a covalent linkage


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529831% PEG MME 5000, 0.1 M MES, 0.2 M ammonium sulfate, 0.01 M cadmium chloride, 0.01 M sodium hepes, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3347.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.819α = 90
b = 46.919β = 90
c = 62.089γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2005-11-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.54

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
11.937.5394.140.04527.16.39100489459
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)
11.91.949650.1188.53.85

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)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 REPLACEMENTTHROUGHOUT1.937.5310048945947494.140.19620.196190.193980.24028RANDOM21.266
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]
-0.3-0.430.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.118
r_scangle_it4.684
r_scbond_it2.948
r_mcangle_it1.975
r_angle_refined_deg1.699
r_mcbond_it1.06
r_angle_other_deg1.05
r_symmetry_hbond_refined0.397
r_symmetry_vdw_refined0.379
r_symmetry_vdw_other0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.118
r_scangle_it4.684
r_scbond_it2.948
r_mcangle_it1.975
r_angle_refined_deg1.699
r_mcbond_it1.06
r_angle_other_deg1.05
r_symmetry_hbond_refined0.397
r_symmetry_vdw_refined0.379
r_symmetry_vdw_other0.304
r_xyhbond_nbd_refined0.286
r_nbd_other0.249
r_nbd_refined0.243
r_chiral_restr0.114
r_nbtor_other0.087
r_bond_refined_d0.019
r_gen_planes_refined0.019
r_gen_planes_other0.019
r_metal_ion_refined0.01
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
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 Atoms964
Nucleic Acid Atoms
Solvent Atoms81
Heterogen Atoms51

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
AMoREphasing