3GUI

T4 lysozyme M102E/L99A mutant with buried charge in apolar cavity--Apo structure


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DMV 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP827730% PEG 8000, 0.20M ammonium sulfate, 0.10M Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.0339.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.769α = 90
b = 48.769β = 90
c = 128.51γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Double crystal Si(111)2007-10-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.1ALS8.2.1

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
11.4545.699.80.036426.7284302
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)
11.451.51000.286.36.6

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 REPLACEMENTTHROUGHOUT3DMV1.4538.8426915143399.750.185580.184510.20648RANDOM19.335
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]
0.050.05-0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.578
r_dihedral_angle_4_deg17.613
r_dihedral_angle_3_deg12.34
r_dihedral_angle_1_deg4.719
r_scangle_it3.719
r_scbond_it2.354
r_angle_refined_deg1.351
r_mcangle_it1.33
r_mcbond_it0.912
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.578
r_dihedral_angle_4_deg17.613
r_dihedral_angle_3_deg12.34
r_dihedral_angle_1_deg4.719
r_scangle_it3.719
r_scbond_it2.354
r_angle_refined_deg1.351
r_mcangle_it1.33
r_mcbond_it0.912
r_nbtor_refined0.309
r_symmetry_vdw_refined0.307
r_symmetry_hbond_refined0.22
r_nbd_refined0.201
r_xyhbond_nbd_refined0.12
r_chiral_restr0.082
r_bond_refined_d0.011
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 Atoms1297
Nucleic Acid Atoms
Solvent Atoms206
Heterogen Atoms24

Software

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