3MGW

Thermodynamics and structure of a salmon cold-active goose-type lysozyme


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 153LPDB ENTRY 153L

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29543-45 % ammonium sulphate, 0.01M cobalt chloride, 0.1M MES , pH 6.25-6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.4649.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.15α = 90
b = 103.15β = 90
c = 48.67γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2007-12-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.91841BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.7542.7699.60.0880.08811.33.61941019410220.38
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.8499.90.490.491.53.62840

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 153L1.7542.761841798999.640.1780.1760.215RANDOM24.55
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]
-0.23-0.12-0.230.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.821
r_dihedral_angle_4_deg24.174
r_dihedral_angle_3_deg13.596
r_dihedral_angle_1_deg5.353
r_scangle_it3.584
r_scbond_it2.368
r_mcangle_it1.581
r_angle_refined_deg1.298
r_mcbond_it0.987
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.821
r_dihedral_angle_4_deg24.174
r_dihedral_angle_3_deg13.596
r_dihedral_angle_1_deg5.353
r_scangle_it3.584
r_scbond_it2.368
r_mcangle_it1.581
r_angle_refined_deg1.298
r_mcbond_it0.987
r_nbtor_refined0.307
r_symmetry_hbond_refined0.216
r_nbd_refined0.207
r_xyhbond_nbd_refined0.135
r_symmetry_vdw_refined0.123
r_chiral_restr0.091
r_bond_refined_d0.014
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1429
Nucleic Acid Atoms
Solvent Atoms148
Heterogen Atoms6

Software

Software
Software NamePurpose
MAR345data collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling