2ZIJ

Crystal Structure of Human Lysozyme Expressed in E. coli.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62772.5M sodium chloride, 0.03M phosphate, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
1.9938.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.6α = 90
b = 61β = 90
c = 33.9γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray277IMAGE PLATERIGAKU RAXIS IICdouble-mirror1999-04-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

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
11.941.588.10.078207288599

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 1I1Z1.941.5818541088.140.170820.167460.23541RANDOM13.927
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]
-0.12-0.921.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.976
r_dihedral_angle_3_deg13.376
r_dihedral_angle_4_deg13.213
r_dihedral_angle_1_deg6.436
r_scangle_it4.22
r_scbond_it2.539
r_angle_refined_deg1.522
r_mcangle_it1.362
r_mcbond_it0.776
r_nbtor_refined0.299
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.976
r_dihedral_angle_3_deg13.376
r_dihedral_angle_4_deg13.213
r_dihedral_angle_1_deg6.436
r_scangle_it4.22
r_scbond_it2.539
r_angle_refined_deg1.522
r_mcangle_it1.362
r_mcbond_it0.776
r_nbtor_refined0.299
r_symmetry_hbond_refined0.223
r_nbd_refined0.222
r_symmetry_vdw_refined0.188
r_xyhbond_nbd_refined0.177
r_chiral_restr0.108
r_metal_ion_refined0.103
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1029
Nucleic Acid Atoms
Solvent Atoms131
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing