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- PDB-5ni1: CryoEM structure of haemoglobin at 3.2 A determined with the Volt... -

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Basic information

Entry
Database: PDB / ID: 5ni1
TitleCryoEM structure of haemoglobin at 3.2 A determined with the Volta phase plate
DescriptorHemoglobin subunit alpha, Hemoglobin subunit beta
KeywordsOXYGEN TRANSPORT / Volta phase plate / Single particle analysis / Hemoglobin / oxygen transport
Specimen sourceHomo sapiens / human
MethodElectron microscopy (3.2 Å resolution / Particle / Single particle)
AuthorsKhoshouei, M. / Radjainia, M. / Bunker, R. / Baumeister, W. / Danev, R.
CitationElife, 2016, 5

Elife, 2016, 5 Yorodumi Papers
Cryo-EM single particle analysis with the Volta phase plate.
Radostin Danev / Wolfgang Baumeister

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 22, 2017 / Release: Apr 12, 2017

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Assembly

Deposited unit
A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
C: Hemoglobin subunit alpha
D: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5478
Polyers62,0814
Non-polymers2,4664
Water43224
#1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Polypeptide(L)Hemoglobin subunit alpha / Alpha-globin / Hemoglobin alpha chain


Mass: 15150.353 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens / human / References: UniProt: P69905

Cellular component

Molecular function

Biological process

#2: Polypeptide(L)Hemoglobin subunit beta / Beta-globin / Hemoglobin beta chain


Mass: 15890.198 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens / human / References: UniProt: P68871

Cellular component

Molecular function

Biological process

#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Formula: C34H32FeN4O4
#4: WaterChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: Hemoglobin / Type: COMPLEX / Entity ID: 1, 2, 3 / Source: NATURAL
Source (natural)Organism: Homo sapiens
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: REFMAC / Version: 5.8.0158 / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 175300 / Symmetry type: POINT
Refine
Refine IDB iso meanAniso B11Aniso B12Aniso B13Aniso B22Aniso B23Aniso B33Correlation coeff Fo to FcDetailsR factor R workR factor obsHighest resolutionLowest resolutionNumber reflection obsPercent reflection obsOverall SU BOverall SU MLOverall ESU RStereochemistry target valuesSolvent model details
160.032-1.39-1.67-0.010.67-0.010.720.574HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS0.370770.370773.20105.0074004100.0018.1680.2780.340MAXIMUM LIKELIHOOD WITH PHASESPARAMETERS FOR MASK CACLULATION
ELECTRON MICROSCOPY
Number of atoms included #1Total: 4580
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0100.0194703
ELECTRON MICROSCOPYr_bond_other_d0.0020.0204331
ELECTRON MICROSCOPYr_angle_refined_deg1.5322.0006449
ELECTRON MICROSCOPYr_angle_other_deg1.2963.00010003
ELECTRON MICROSCOPYr_dihedral_angle_1_deg5.7125.000570
ELECTRON MICROSCOPYr_dihedral_angle_2_deg33.07723.889180
ELECTRON MICROSCOPYr_dihedral_angle_3_deg12.44615.000705
ELECTRON MICROSCOPYr_dihedral_angle_4_deg11.35715.00012
ELECTRON MICROSCOPYr_chiral_restr0.1040.200708
ELECTRON MICROSCOPYr_gen_planes_refined0.0060.0215272
ELECTRON MICROSCOPYr_gen_planes_other0.0030.020984
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it5.5645.6852292
ELECTRON MICROSCOPYr_mcbond_other5.5205.6732291
ELECTRON MICROSCOPYr_mcangle_it9.8188.4842858
ELECTRON MICROSCOPYr_mcangle_other9.8338.4962859
ELECTRON MICROSCOPYr_scbond_it7.1026.4952411
ELECTRON MICROSCOPYr_scbond_other7.0916.4922409
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other12.7439.2523591
ELECTRON MICROSCOPYr_long_range_B_refined18.71764.9355272
ELECTRON MICROSCOPYr_long_range_B_other18.72164.9435273
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS restraints ncs

Refine ID: ELECTRON MICROSCOPY / Type: tight thermal / Weight position: 0.5

Dom IDAuth asym IDEns IDNumberRms dev position
1A110680.34
2B211230.12
Refine LS shellHighest resolution: 3.2 Å / R factor R work: 0.965 / Lowest resolution: 3.283 Å / Number reflection R free: 0 / Number reflection R work: 5475 / Total number of bins used: 20 / Percent reflection obs: 1

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