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- PDB-4htk: Mitigation of X-ray damage in macromolecular crystallography by s... -

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Basic information

Entry
Database: PDB / ID: 4htk
TitleMitigation of X-ray damage in macromolecular crystallography by submicrometer line focusing; total dose 2.17 x 10e+12 X-ray photons
ComponentsLysozyme C
KeywordsHYDROLASE / O-GLYCOSYL / GLYCOSIDASE / CYTOPLASM (WHITE)
Function / homology
Function and homology information


Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm
Similarity search - Function
Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily ...Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsDuke, N.E.C. / Finfrock, Y.Z. / Stern, E.A. / Alkire, R.W. / Lazarski, K. / Joachimiak, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Mitigation of X-ray damage in macromolecular crystallography by submicrometre line focusing.
Authors: Finfrock, Y.Z. / Stern, E.A. / Alkire, R.W. / Kas, J.J. / Evans-Lutterodt, K. / Stein, A. / Duke, N. / Lazarski, K. / Joachimiak, A.
History
DepositionNov 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,82413
Polymers14,3311
Non-polymers49312
Water3,153175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.022, 79.022, 36.907
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-428-

HOH

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Components

#1: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.01 Å3/Da / Density % sol: 38.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.73
Details: 0.100M sodium acetate, pH 4.73, 5% sodium chloride, w/v, 25% ethylene glycol, v/v, micro-seeded, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.66658 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 28, 2012
RadiationMonochromator: Si (111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.66658 Å / Relative weight: 1
ReflectionResolution: 1.2→55.877 Å / Num. all: 36830 / Num. obs: 36830 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 8.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allDiffraction-ID% possible all
1.2-1.216.10.527898199.9
1.21-1.226.30.548890196.7
1.22-1.236.40.496887196.3
1.23-1.246.20.489101100
1.24-1.256.20.464900199.9
1.25-1.276.50.458884196.4
1.27-1.286.40.404914197.8
1.28-1.296.40.3698781100
1.29-1.316.40.351915198.8
1.31-1.326.50.365909196.4
1.32-1.346.60.3318911100
1.34-1.356.30.3149151100
1.35-1.376.70.305897196
1.37-1.396.80.2759041100
1.39-1.46.60.2529181100
1.4-1.426.80.244886196.6
1.42-1.446.80.215914199.9
1.44-1.466.70.204918199.8
1.46-1.496.90.186901197.4
1.49-1.516.90.1719111100
1.51-1.546.90.159907197.9
1.54-1.5770.147912199.9
1.57-1.670.138929199.9
1.6-1.637.20.124902198.3
1.63-1.667.10.119211100
1.66-1.77.20.107919198.6
1.7-1.757.10.1019391100
1.75-1.797.20.091903198.8
1.79-1.857.10.084936199.3
1.85-1.97.20.072917199.9
1.9-1.977.10.065942199.4
1.97-2.057.10.057925199.5
2.05-2.1570.0519331100
2.15-2.266.90.044943199.7
2.26-2.46.80.037942199.7
2.4-2.596.80.032952199.8
2.59-2.856.70.028964199.7
2.85-3.267.20.023961199.9
3.26-4.16.90.029901100
4.1-1006.40.0191053198.1

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→27.938 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.9313 / SU ML: 0.19 / σ(F): 1.34 / Phase error: 12.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1516 1837 4.99 %
Rwork0.1335 34949 -
obs0.1344 36786 99.06 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.503 Å2 / ksol: 0.346 e/Å3
Displacement parametersBiso max: 38.53 Å2 / Biso mean: 12.2577 Å2 / Biso min: 4.41 Å2
Baniso -1Baniso -2Baniso -3
1-0.5092 Å2-0 Å20 Å2
2--0.5092 Å2-0 Å2
3----1.0185 Å2
Refinement stepCycle: LAST / Resolution: 1.2→27.938 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 21 175 1197
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081128
X-RAY DIFFRACTIONf_angle_d1.2111529
X-RAY DIFFRACTIONf_chiral_restr0.086159
X-RAY DIFFRACTIONf_plane_restr0.005201
X-RAY DIFFRACTIONf_dihedral_angle_d11.466434
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1996-1.23210.21121310.18812615274698
1.2321-1.26830.2031220.16032646276899
1.2683-1.30930.14551250.13712640276599
1.3093-1.35610.16741480.13482632278099
1.3561-1.41040.16281260.11542665279199
1.4104-1.47450.16441390.10892629276898
1.4745-1.55230.12211390.10222669280899
1.5523-1.64950.12141410.10492672281399
1.6495-1.77690.14441450.11312691283699
1.7769-1.95560.15081600.121626812841100
1.9556-2.23850.14561630.124427192882100
2.2385-2.81990.15061400.1427862926100
2.8199-27.94610.15261580.153229043062100

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