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- PDB-6wem: Crimson 0.9 -

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Basic information

Entry
Database: PDB / ID: 6wem
TitleCrimson 0.9
ComponentsmCrimson 0.9
KeywordsFLUORESCENT PROTEIN / engineered protein
Biological speciesEntacmaea quadricolor (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsAtaie, N. / Tran Tang, C. / Sens, A. / Lin, M.Z. / Chu, J. / Ng, H.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1833181 United States
CitationJournal: To Be Published
Title: Crimson 0.9
Authors: Ataie, N. / Tran Tang, C. / Sens, A. / Lin, M.Z. / Chu, J.
History
DepositionApr 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: mCrimson 0.9
B: mCrimson 0.9
C: mCrimson 0.9
D: mCrimson 0.9


Theoretical massNumber of molelcules
Total (without water)102,2694
Polymers102,2694
Non-polymers00
Water3,657203
1
A: mCrimson 0.9


Theoretical massNumber of molelcules
Total (without water)25,5671
Polymers25,5671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: mCrimson 0.9


Theoretical massNumber of molelcules
Total (without water)25,5671
Polymers25,5671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: mCrimson 0.9


Theoretical massNumber of molelcules
Total (without water)25,5671
Polymers25,5671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: mCrimson 0.9


Theoretical massNumber of molelcules
Total (without water)25,5671
Polymers25,5671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.546, 90.046, 129.518
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
mCrimson 0.9


Mass: 25567.150 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entacmaea quadricolor (sea anemone) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: obtained synthetically / Formula: H2O
Has ligand of interestY

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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: 2.07 Å3/Da / Density % sol: 40.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M MgCl2, 0.1 M Bis-Tris HCl pH 6.5, and 25% PEG 3350

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.04→40 Å / Num. obs: 53213 / % possible obs: 99.1 % / Redundancy: 7.05 % / Rsym value: 0.108 / Net I/σ(I): 12.12
Reflection shellResolution: 2.04→2.16 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 8162 / Rsym value: 0.874

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IP2

3ip2


Resolution: 2.04→40 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.933 / SU B: 11.626 / SU ML: 0.146 / Cross valid method: FREE R-VALUE / ESU R: 0.24 / ESU R Free: 0.188
Details: HYDROGENS HAVE BEEN ADDED IN THEIR RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.235 2710 5.095 %
Rwork0.191 --
obs-53190 99 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.873 Å20 Å20 Å2
2---0.494 Å20 Å2
3----0.379 Å2
Refinement stepCycle: LAST / Resolution: 2.04→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7128 0 0 203 7331
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0137461
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176775
X-RAY DIFFRACTIONr_angle_refined_deg1.971.67310081
X-RAY DIFFRACTIONr_angle_other_deg1.4091.59215823
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6775912
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.44323.137373
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.823151279
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1621533
X-RAY DIFFRACTIONr_chiral_restr0.0820.2910
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.028364
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021551
X-RAY DIFFRACTIONr_nbd_refined0.2030.21256
X-RAY DIFFRACTIONr_nbd_other0.2870.2113
X-RAY DIFFRACTIONr_nbtor_refined0.1720.23338
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2252
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.792.1423627
X-RAY DIFFRACTIONr_mcbond_other1.792.1413626
X-RAY DIFFRACTIONr_mcangle_it2.6833.1964546
X-RAY DIFFRACTIONr_mcangle_other2.6833.1974547
X-RAY DIFFRACTIONr_scbond_it2.9832.5943834
X-RAY DIFFRACTIONr_scbond_other2.9832.5953835
X-RAY DIFFRACTIONr_scangle_it4.7673.7235535
X-RAY DIFFRACTIONr_scangle_other4.7673.7235535
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.04→2.1 Å
RfactorNum. reflection% reflection
Rfree0.283 164 -
Rwork0.284 3346 -
obs--89.56 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.013-0.15890.30651.2242-0.32621.01970.03990.10930.0295-0.0998-0.0846-0.1224-0.02630.14340.04460.13120.0190.0080.03690.03880.10458.437211.497134.7945
21.4164-0.0832-0.15750.6883-0.12971.2579-0.0688-0.07690.00140.06060.04470.07730.1-0.00160.02410.16140.0011-0.0270.00730.01170.086155.16680.122862.6497
31.69210.29320.08451.13850.31471.1473-0.0133-0.30540.00480.1650.00390.05960.0648-0.12490.00940.1550.02460.01120.08460.00690.009923.31671.225260.1084
41.3043-0.0735-0.25991.24520.39811.09250.04390.08450.0694-0.2125-0.01830.0606-0.1011-0.0894-0.02560.15550.0147-0.00480.01190.0010.04927.02577.203630.4416
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 232
2X-RAY DIFFRACTION2B7 - 232
3X-RAY DIFFRACTION3C7 - 231
4X-RAY DIFFRACTION4D8 - 231

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