2HZ1

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RTXpdb entry 1RTX

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
2.2645.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.662α = 90
b = 46.503β = 90
c = 62.621γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2005-10-01MSINGLE 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)R Sym 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
11.837.2799.930.0460.2486.831144311435
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)
11.81.86990.1439.66.68

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUTpdb entry 1RTX1.837.27114431143559899.930.19120.191170.188750.2385RANDOM18.3
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]
-0.09-0.730.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.345
r_scangle_it4.181
r_scbond_it2.71
r_mcangle_it1.723
r_angle_refined_deg1.596
r_angle_other_deg0.958
r_mcbond_it0.946
r_symmetry_vdw_refined0.331
r_symmetry_vdw_other0.285
r_xyhbond_nbd_refined0.267
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.345
r_scangle_it4.181
r_scbond_it2.71
r_mcangle_it1.723
r_angle_refined_deg1.596
r_angle_other_deg0.958
r_mcbond_it0.946
r_symmetry_vdw_refined0.331
r_symmetry_vdw_other0.285
r_xyhbond_nbd_refined0.267
r_nbd_refined0.256
r_nbd_other0.238
r_symmetry_hbond_refined0.226
r_chiral_restr0.1
r_nbtor_other0.091
r_bond_refined_d0.016
r_gen_planes_refined0.016
r_gen_planes_other0.016
r_metal_ion_refined0.011
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms969
Nucleic Acid Atoms
Solvent Atoms130
Heterogen Atoms55

Software

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