4NEB

Previously de-ionized HEW lysozyme batch crystallized in 0.5 M MnCl2


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.5293Previously de-ionized lysozyme, no buffer added, 0.5 M MnCl2, pH 4.5, batch crystallization, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0640.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.186α = 90
b = 79.186β = 90
c = 37.715γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray295IMAGE PLATEMAR scanner 345 mm plate2000-12-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLURE BEAMLINE DW32LUREDW32

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.4827.30899.90.0458.12057517.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.481.531000.4047.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 193L1.4827.3083816018522200599.840.124920.12210.15117RANDOM22.273
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]
-0.18-0.180.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.321
r_sphericity_free24.123
r_dihedral_angle_4_deg23.067
r_dihedral_angle_3_deg14.452
r_sphericity_bonded10.644
r_dihedral_angle_1_deg5.428
r_rigid_bond_restr2.751
r_scbond_it2.558
r_mcangle_it1.939
r_mcbond_it1.494
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.321
r_sphericity_free24.123
r_dihedral_angle_4_deg23.067
r_dihedral_angle_3_deg14.452
r_sphericity_bonded10.644
r_dihedral_angle_1_deg5.428
r_rigid_bond_restr2.751
r_scbond_it2.558
r_mcangle_it1.939
r_mcbond_it1.494
r_mcbond_other1.484
r_angle_refined_deg1.35
r_angle_other_deg0.851
r_chiral_restr0.096
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_gen_planes_other0.002
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1001
Nucleic Acid Atoms
Solvent Atoms62
Heterogen Atoms3

Software

Software
Software NamePurpose
REFMACrefinement
AMoREphasing
CNSrefinement
HKL-2000data reduction
TRUNCATEdata reduction
SCALEPACKdata scaling
HKL-2000data collection