4NHI

Crystal structure of Hen egg-white lysozyme in Tris buffer at pH 7.5 with Magnesium formate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2LYZ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.527780mg/ml hen egg-white lysozyme, 100mM TrisHCl, 0.4M Mg-Formate(0.2~0.6 M), pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
1.935.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.594α = 90
b = 76.594β = 90
c = 37.065γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702013-07-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 6C1PAL/PLS6C1

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
11.345099.80.1370.13759.72411.1349012349012-3
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)
11.341.3699.70.5360.5361.6

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 REPLACEMENTTHROUGHOUT2LYZ1.3438.324101129099.630.169670.167180.21821RANDOM19.282
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]
-11.21-11.2122.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.396
r_sphericity_free30.514
r_dihedral_angle_4_deg17.226
r_sphericity_bonded15.632
r_dihedral_angle_3_deg14.265
r_dihedral_angle_1_deg6.012
r_rigid_bond_restr5.634
r_angle_refined_deg2.04
r_angle_other_deg1.184
r_chiral_restr0.149
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.396
r_sphericity_free30.514
r_dihedral_angle_4_deg17.226
r_sphericity_bonded15.632
r_dihedral_angle_3_deg14.265
r_dihedral_angle_1_deg6.012
r_rigid_bond_restr5.634
r_angle_refined_deg2.04
r_angle_other_deg1.184
r_chiral_restr0.149
r_bond_refined_d0.022
r_gen_planes_refined0.012
r_gen_planes_other0.003
r_bond_other_d0.001
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1000
Nucleic Acid Atoms
Solvent Atoms126
Heterogen Atoms

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling