3A96

Crystal structure of hen egg white lysozyme soaked with 100mM RhCl3 at pH2.2


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.5293sodium chloride, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.9737.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.967α = 90
b = 77.967β = 90
c = 37.14γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS VII2008-12-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
11.758096.10.06521.51166522.778
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)
1.751.81980.32521.5

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 193L1.7518.381106956396.260.195260.193760.2245RANDOM19.6
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.592
r_dihedral_angle_4_deg14.32
r_dihedral_angle_3_deg13.6
r_sphericity_free8.579
r_dihedral_angle_1_deg5.883
r_scangle_it3.365
r_scbond_it2.141
r_mcangle_it1.385
r_angle_refined_deg1.357
r_mcbond_it0.776
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.592
r_dihedral_angle_4_deg14.32
r_dihedral_angle_3_deg13.6
r_sphericity_free8.579
r_dihedral_angle_1_deg5.883
r_scangle_it3.365
r_scbond_it2.141
r_mcangle_it1.385
r_angle_refined_deg1.357
r_mcbond_it0.776
r_nbtor_refined0.3
r_symmetry_vdw_refined0.249
r_nbd_refined0.213
r_symmetry_hbond_refined0.118
r_xyhbond_nbd_refined0.115
r_chiral_restr0.11
r_metal_ion_refined0.1
r_bond_refined_d0.012
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1019
Nucleic Acid Atoms
Solvent Atoms91
Heterogen Atoms9

Software

Software
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling