2RBO

2-nitrothiophene in complex with T4 lysozyme L99A/M102Q


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.12772.2M sodium-potassium phosphate, 0.05M beta-mercaptoethanol, 0.05M 2-hydroxyethyldisulfide, pH 7.1, vapor diffusion, hanging drop, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.7455.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.107α = 90
b = 60.107β = 90
c = 96.715γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC QUANTUM 315Vertical focusing mirror; single crystal Si(311) bent monochromator (horizontal focusing)2006-12-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-10.979462SSRLBL9-1

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
11.2952.0699.90.06711.87.65158351583
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)
1.291.341000.6227.6

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 REPLACEMENTTHROUGHOUT1LGU1.2952.065153748915262299.930.174330.173350.19319RANDOM14.447
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]
-0.06-0.03-0.060.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.981
r_dihedral_angle_4_deg12.315
r_dihedral_angle_3_deg10.448
r_dihedral_angle_1_deg4.497
r_sphericity_free2.434
r_scangle_it2.089
r_sphericity_bonded1.969
r_scbond_it1.684
r_angle_refined_deg1.216
r_rigid_bond_restr1.144
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.981
r_dihedral_angle_4_deg12.315
r_dihedral_angle_3_deg10.448
r_dihedral_angle_1_deg4.497
r_sphericity_free2.434
r_scangle_it2.089
r_sphericity_bonded1.969
r_scbond_it1.684
r_angle_refined_deg1.216
r_rigid_bond_restr1.144
r_mcangle_it0.989
r_mcbond_it0.631
r_nbtor_refined0.305
r_nbd_refined0.192
r_symmetry_vdw_refined0.137
r_xyhbond_nbd_refined0.111
r_symmetry_hbond_refined0.075
r_chiral_restr0.071
r_bond_refined_d0.007
r_gen_planes_refined0.004
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1331
Nucleic Acid Atoms
Solvent Atoms303
Heterogen Atoms21

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
REFMACphasing