4L2M

Crystal structure of the 2/2 hemoglobin from Synechococcus sp. PCC 7002 in the cyanomet state and with covalently attached heme


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1S69PDB ENTRY 1S69

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP52771% v/v isopropanol, 2 M ammonium sulfate, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.3447.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.622α = 90
b = 40.951β = 111.21
c = 66.461γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MMeridionally-bent fused silica mirror with palladium and uncoated stripes vertically-focusing at 6.6:1 demagnification2013-04-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X250.979NSLSX25

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
12.255099.90.10896123961239643.8
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)
12.252.311000.4563.895.1865

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 1S692.2534.19122791227960999.80.22140.22140.21790.2881RANDOM46.3993
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]
0.451.32-1.160.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.568
r_dihedral_angle_3_deg15.368
r_dihedral_angle_4_deg15.202
r_dihedral_angle_1_deg6.634
r_mcangle_it3.459
r_mcbond_other2.337
r_mcbond_it2.336
r_angle_refined_deg1.7
r_angle_other_deg0.754
r_chiral_restr0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.568
r_dihedral_angle_3_deg15.368
r_dihedral_angle_4_deg15.202
r_dihedral_angle_1_deg6.634
r_mcangle_it3.459
r_mcbond_other2.337
r_mcbond_it2.336
r_angle_refined_deg1.7
r_angle_other_deg0.754
r_chiral_restr0.06
r_gen_planes_other0.016
r_bond_refined_d0.013
r_gen_planes_refined0.012
r_bond_other_d0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1934
Nucleic Acid Atoms
Solvent Atoms37
Heterogen Atoms105

Software

Software
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-2000data reduction