2ZYP

X-ray structure of hen egg-white lysozyme with poly(allyl amine)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LKRPDB ENTRY 1LKR

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72930.1% PAA, 1.0M sodium chloride, 0.1M sodium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.9336.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.94α = 90
b = 76.94β = 90
c = 37.331γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker DIP-60402008-10-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.900SPring-8BL44XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.1818.6695.10.0614.868455
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.181.282.30.1093.62923

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 1LKR1.1818.6633979179195.90.204090.203050.22368RANDOM10.554
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]
-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.635
r_dihedral_angle_3_deg11.803
r_dihedral_angle_4_deg11.331
r_dihedral_angle_1_deg5.311
r_sphericity_free1.4
r_scangle_it1.278
r_sphericity_bonded1.074
r_angle_refined_deg0.998
r_scbond_it0.948
r_mcangle_it0.733
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.635
r_dihedral_angle_3_deg11.803
r_dihedral_angle_4_deg11.331
r_dihedral_angle_1_deg5.311
r_sphericity_free1.4
r_scangle_it1.278
r_sphericity_bonded1.074
r_angle_refined_deg0.998
r_scbond_it0.948
r_mcangle_it0.733
r_rigid_bond_restr0.704
r_mcbond_it0.398
r_nbtor_refined0.294
r_nbd_refined0.2
r_symmetry_vdw_refined0.19
r_metal_ion_refined0.107
r_xyhbond_nbd_refined0.095
r_chiral_restr0.082
r_symmetry_hbond_refined0.073
r_bond_refined_d0.005
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1064
Nucleic Acid Atoms
Solvent Atoms143
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing