3DMV

Free of ligand binding in the hydrophobic cavity of T4 lysozyme L99A mutant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1L90PDB entry 1L90

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.92772.0-2.2 M K/Na phosphate, pH 6.9, 5mM BME and 5mM oxidized BME. Complexes were made by soaking or gas-phase diffusion, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.6653.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.902α = 90
b = 59.902β = 90
c = 95.307γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2005-03-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R1.542

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.655299.42433722
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.651.7198.4

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 REPLACEMENTTHROUGHOUTPDB entry 1L901.6545.5523073123499.460.183980.18260.20952RANDOM
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.014
r_dihedral_angle_4_deg15.998
r_dihedral_angle_3_deg12.825
r_dihedral_angle_1_deg4.832
r_scangle_it2.74
r_scbond_it1.809
r_angle_refined_deg1.084
r_mcangle_it0.98
r_mcbond_it0.614
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.014
r_dihedral_angle_4_deg15.998
r_dihedral_angle_3_deg12.825
r_dihedral_angle_1_deg4.832
r_scangle_it2.74
r_scbond_it1.809
r_angle_refined_deg1.084
r_mcangle_it0.98
r_mcbond_it0.614
r_nbtor_refined0.301
r_nbd_refined0.204
r_symmetry_vdw_refined0.17
r_symmetry_hbond_refined0.136
r_xyhbond_nbd_refined0.132
r_chiral_restr0.066
r_bond_refined_d0.009
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1364
Nucleic Acid Atoms
Solvent Atoms251
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing