3A93

Crystal structure of hen egg white lysozyme soaked with 30mM RhCl3


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
1.9837.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.994α = 90
b = 77.994β = 90
c = 37.259γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS VII2008-12-08MSINGLE 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
11.558099.80.04424.81724218.023
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)
1.551.611000.22425.2

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 193L1.5515.81628986699.690.191370.190510.20676RANDOM17.88
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_deg33.675
r_dihedral_angle_4_deg14.48
r_dihedral_angle_3_deg11.391
r_sphericity_free8.384
r_dihedral_angle_1_deg5.602
r_scangle_it3.301
r_scbond_it2.098
r_mcangle_it1.374
r_angle_refined_deg1.224
r_mcbond_it0.734
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.675
r_dihedral_angle_4_deg14.48
r_dihedral_angle_3_deg11.391
r_sphericity_free8.384
r_dihedral_angle_1_deg5.602
r_scangle_it3.301
r_scbond_it2.098
r_mcangle_it1.374
r_angle_refined_deg1.224
r_mcbond_it0.734
r_nbtor_refined0.301
r_symmetry_vdw_refined0.233
r_nbd_refined0.208
r_xyhbond_nbd_refined0.112
r_chiral_restr0.096
r_symmetry_hbond_refined0.087
r_metal_ion_refined0.085
r_bond_refined_d0.009
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1004
Nucleic Acid Atoms
Solvent Atoms101
Heterogen Atoms13

Software

Software
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling