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- PDB-3u7t: Room temperature ultra-high resolution time-of-flight neutron and... -

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Basic information

Entry
Database: PDB / ID: 3u7t
TitleRoom temperature ultra-high resolution time-of-flight neutron and X-ray diffraction studies of H/D exchanged crambin
ComponentsCrambin
KeywordsPLANT PROTEIN / thionin family
Function / homology
Function and homology information


defense response / extracellular region
Similarity search - Function
Thionin-like / Thionin / Thionin-like superfamily / Plant thionin / Plant thionins signature. / Crambin / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesCrambe hispanica subsp. abyssinica (Abyssinian crambe)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 0.85 Å
AuthorsChen, J.C.-H.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Room-temperature ultrahigh-resolution time-of-flight neutron and X-ray diffraction studies of H/D-exchanged crambin.
Authors: Chen, J.C. / Fisher, Z. / Kovalevsky, A.Y. / Mustyakimov, M. / Hanson, B.L. / Zhurov, V.V. / Langan, P.
History
DepositionOct 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Crambin


Theoretical massNumber of molelcules
Total (without water)4,7281
Polymers4,7281
Non-polymers00
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)22.795, 18.826, 41.042
Angle α, β, γ (deg.)90.00, 90.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide Crambin /


Mass: 4728.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Crambe hispanica subsp. abyssinica (Abyssinian crambe)
References: UniProt: P01542
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.86 Å3/Da / Density % sol: 33.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Vapor diffusion of protein in 80 % EtOH solution against a 55 % EtOH solution, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 0.71073 Å
DetectorType: RIGAKU RAPID / Detector: IMAGE PLATE / Date: Nov 7, 2010
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.71073 Å / Relative weight: 1
ReflectionResolution: 0.85→30 Å / Num. all: 31025 / Num. obs: 30963 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.41 % / Biso Wilson estimate: 6.3 Å2 / Rsym value: 0.05 / Net I/σ(I): 8.2
Reflection shellResolution: 0.85→0.88 Å / Redundancy: 3.21 % / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 1.9 / Num. unique all: 3065 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7_650)refinement
d*TREKdata reduction
d*TREKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CRN

1crn


Resolution: 0.85→9.898 Å / SU ML: 0.07 / σ(F): 0 / Phase error: 12.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.136 1541 5.03 %Random
Rwork0.1194 ---
all0.1202 31025 --
obs0.1202 30659 98.85 %-
Solvent computationShrinkage radii: 0.17 Å / VDW probe radii: 0.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80 Å2 / ksol: 0.6 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.0266 Å2-0 Å20.3426 Å2
2---0.1106 Å2-0 Å2
3---0.084 Å2
Refine analyzeLuzzati coordinate error obs: 0.07 Å
Refinement stepCycle: LAST / Resolution: 0.85→9.898 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms341 0 0 51 392
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008353
X-RAY DIFFRACTIONf_angle_d1.38485
X-RAY DIFFRACTIONf_dihedral_angle_d8.975125
X-RAY DIFFRACTIONf_chiral_restr0.07559
X-RAY DIFFRACTIONf_plane_restr0.0165
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.85-0.87750.20591370.19612602X-RAY DIFFRACTION98
0.8775-0.90880.18791430.17562589X-RAY DIFFRACTION98
0.9088-0.94520.18051390.15582652X-RAY DIFFRACTION99
0.9452-0.98810.1751350.142632X-RAY DIFFRACTION99
0.9881-1.04020.13971420.12262633X-RAY DIFFRACTION99
1.0402-1.10530.1091350.11512658X-RAY DIFFRACTION99
1.1053-1.19050.09611380.10152652X-RAY DIFFRACTION99
1.1905-1.310.1221420.09892639X-RAY DIFFRACTION99
1.31-1.49910.1131390.10152667X-RAY DIFFRACTION99
1.4991-1.88650.1241440.10672677X-RAY DIFFRACTION98
1.8865-9.89840.14781470.12382717X-RAY DIFFRACTION98

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