3HT9

2-methoxyphenol in complex with T4 lysozyme L99A/M102Q


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LGUPDB ENTRY 1LGU

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52772.2M sodium-potassium phosphate, 0.05M beta-mercaptoethanol, 0.05M 2-hydroxyethyldisulfide, pH 6.5, vapor diffusion, hanging drop, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.754.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.09α = 90
b = 60.09β = 90
c = 96.45γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray296CCDADSC QUANTUM 315r2008-07-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.11589ALS8.3.1

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
12.023099.90.09918.178.911372713727
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)
12.022.1599.90.3745.99.14

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 DIFFRACTIONREFMACTHROUGHOUTPDB ENTRY 1LGU2.0228.6913725134502751000.172220.171270.21934RANDOM17.67
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]
0.050.020.05-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.528
r_dihedral_angle_3_deg14.166
r_dihedral_angle_4_deg12.992
r_dihedral_angle_1_deg5.358
r_scangle_it3.49
r_scbond_it2.434
r_angle_refined_deg1.423
r_mcangle_it1.386
r_mcbond_it0.909
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.528
r_dihedral_angle_3_deg14.166
r_dihedral_angle_4_deg12.992
r_dihedral_angle_1_deg5.358
r_scangle_it3.49
r_scbond_it2.434
r_angle_refined_deg1.423
r_mcangle_it1.386
r_mcbond_it0.909
r_nbtor_refined0.308
r_nbd_refined0.213
r_symmetry_hbond_refined0.173
r_symmetry_vdw_refined0.166
r_xyhbond_nbd_refined0.144
r_chiral_restr0.1
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1292
Nucleic Acid Atoms
Solvent Atoms169
Heterogen Atoms23

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
XDSdata reduction
XDSdata scaling
REFMACphasing