4B4E

1.00 A Structure of Lysozyme Crystallized with (R)-2-methyl-2,4- pentanediol


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8277CRYSTALLIZATION BY HANGING DROP AT 4C. CONDITIONS IN DROP: PROTEIN AT 35 MG/ML IN 200MM TRIS (PH 8.0) AND 60% V/V (R)-MPD. CONDITIONS IN RESERVOIR: 200MM TRIS (PH 8.0).
Crystal Properties
Matthews coefficientSolvent content
2.0339.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.53α = 90
b = 77.53β = 90
c = 37.895γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDTOROIDAL FOCUSING MIRROR2011-04-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X6ANSLSX6A

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
111599.30.0743.313.7623972
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)
111.02990.822.5111.2

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 REPLACEMENTTHROUGHOUTINHOUSE MODEL113.359136315599.220.124630.123640.14355RANDOM11.238
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]
-0.53-0.531.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.616
r_sphericity_free19.02
r_dihedral_angle_4_deg14.1
r_dihedral_angle_3_deg11.715
r_sphericity_bonded6.962
r_dihedral_angle_1_deg5.723
r_angle_refined_deg1.306
r_rigid_bond_restr1.203
r_angle_other_deg0.938
r_chiral_restr0.083
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.616
r_sphericity_free19.02
r_dihedral_angle_4_deg14.1
r_dihedral_angle_3_deg11.715
r_sphericity_bonded6.962
r_dihedral_angle_1_deg5.723
r_angle_refined_deg1.306
r_rigid_bond_restr1.203
r_angle_other_deg0.938
r_chiral_restr0.083
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_symmetry_metal_ion_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_nbd_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_nbd_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_nbtor_refined
r_nbtor_other
r_symmetry_vdw_refined
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1000
Nucleic Acid Atoms
Solvent Atoms179
Heterogen Atoms19

Software

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