4NGY

Dialyzed HEW lysozyme batch crystallized in 0.75 M YbCl3 and collected at 100 K


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 193LPDB ENTRY 193L

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.5293Dialyzed lysozyme, no buffer added, 0.75 M YbCl3, pH 4.5, EVAPORATION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0138.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.666α = 90
b = 78.666β = 90
c = 37.151γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MMIRRORS2013-05-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-1ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.3535.1899.10.06112.84.24846516.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.351.4398.50.3262.93.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 193L1.3555.634649023404252499.020.193040.190610.21586RANDOM21.322
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]
0.720.72-1.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.316
r_dihedral_angle_3_deg15.118
r_dihedral_angle_4_deg14.66
r_dihedral_angle_1_deg5.985
r_scbond_it3.907
r_mcangle_it2.343
r_mcbond_it1.755
r_angle_refined_deg1.697
r_mcbond_other1.668
r_angle_other_deg0.954
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.316
r_dihedral_angle_3_deg15.118
r_dihedral_angle_4_deg14.66
r_dihedral_angle_1_deg5.985
r_scbond_it3.907
r_mcangle_it2.343
r_mcbond_it1.755
r_angle_refined_deg1.697
r_mcbond_other1.668
r_angle_other_deg0.954
r_chiral_restr0.124
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d0.003
r_gen_planes_other0.003
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1001
Nucleic Acid Atoms
Solvent Atoms145
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
PHASERphasing
CNSrefinement
XDSdata reduction
XDSdata scaling
TRUNCATEdata scaling
MxCuBEdata collection