4N8Z

In situ lysozyme crystallized on a MiTeGen micromesh with benzamidine ligand


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LYZPDB ENTRY 1LYZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1In situ crystallization on micromesh4.62904% sodium chloride, 100mM sodium acetate pH 4.6, 120mg/ml, In situ crystallization on micromesh, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
1.9837.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.15α = 90
b = 79.15β = 90
c = 36.28γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-10-13MSINGLE WAVELENGTH
21
31
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X12C1.1NSLSX12C
2SYNCHROTRONNSLS BEAMLINE X29A1.075NSLSX29A
3SYNCHROTRONNSLS BEAMLINE X251.1NSLSX25

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
11.226.7697.780.07930.461.9347753400321
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)
11.297.780.0790.07930.461.934003

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1LYZ1.226.7623477534003179597.780.230070.230070.229020.25073RANDOM19.173
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]
-1.2-1.22.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.641
r_dihedral_angle_4_deg17.865
r_dihedral_angle_3_deg14.319
r_dihedral_angle_1_deg7.231
r_long_range_B_refined6.524
r_long_range_B_other5.964
r_scangle_other3.811
r_scbond_it2.63
r_scbond_other2.628
r_angle_refined_deg2.441
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.641
r_dihedral_angle_4_deg17.865
r_dihedral_angle_3_deg14.319
r_dihedral_angle_1_deg7.231
r_long_range_B_refined6.524
r_long_range_B_other5.964
r_scangle_other3.811
r_scbond_it2.63
r_scbond_other2.628
r_angle_refined_deg2.441
r_mcangle_other1.976
r_mcangle_it1.96
r_mcbond_it1.57
r_mcbond_other1.51
r_angle_other_deg1.131
r_chiral_restr0.168
r_bond_refined_d0.029
r_gen_planes_refined0.014
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1001
Nucleic Acid Atoms
Solvent Atoms218
Heterogen Atoms24

Software

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