4NGJ

Dialyzed HEW lysozyme batch crystallized in 1.0 M RbCl and collected at 100 K


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.5293Dialyzed lysozyme, no buffer added, 1.0 M RbCl, pH 4.5, Batch crystallization, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0339.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.024α = 90
b = 79.024β = 90
c = 37.216γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MMIRRORS2013-05-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

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
11.139.512990.03916.54.49062411
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)
11.11.1798.30.2993.24.1

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 193L1.139.5127534543312466999.170.145660.142680.17327RANDOM15.094
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]
-0.27-0.270.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.006
r_sphericity_free28.554
r_dihedral_angle_4_deg19.253
r_dihedral_angle_3_deg12.404
r_sphericity_bonded8.874
r_dihedral_angle_1_deg5.922
r_rigid_bond_restr3.46
r_scbond_it1.833
r_angle_refined_deg1.68
r_mcangle_it1.654
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.006
r_sphericity_free28.554
r_dihedral_angle_4_deg19.253
r_dihedral_angle_3_deg12.404
r_sphericity_bonded8.874
r_dihedral_angle_1_deg5.922
r_rigid_bond_restr3.46
r_scbond_it1.833
r_angle_refined_deg1.68
r_mcangle_it1.654
r_mcbond_it1.371
r_mcbond_other1.367
r_angle_other_deg0.926
r_chiral_restr0.107
r_bond_refined_d0.014
r_gen_planes_refined0.009
r_gen_planes_other0.003
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 Atoms165
Heterogen Atoms3

Software

Software
Software NamePurpose
REFMACrefinement
PHASERphasing
CNSrefinement
XDSdata reduction
XDSdata scaling
TRUNCATEdata scaling
MxCuBEdata collection