3GUJ | pdb_00003guj

T4 lysozyme M102E/L99A mutant with buried charge in apolar cavity--Benzene binding

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3GUI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	277	30% PEG 8000, 0.2M ammounium sulfate, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.814	α = 90
b = 48.814	β = 90
c = 128.369	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315	Si(111)	2007-10-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	1.000	ALS	8.2.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.6	45.644	92.5	0.065	19.1	6		19653		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.66	96.2		0.398	3.9	6.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3GUI	1.6	45.64	18627	1008	92.6	0.20425	0.20243	0.2	0.23884	0.24	RANDOM	25.532

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]
-0.18			-0.18		0.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.741
r_dihedral_angle_4_deg	18.758
r_dihedral_angle_3_deg	12.819
r_dihedral_angle_1_deg	4.977
r_scangle_it	2.86
r_scbond_it	1.854
r_angle_refined_deg	1.152
r_mcangle_it	1.031
r_mcbond_it	0.714
r_nbtor_refined	0.304
r_nbd_refined	0.194
r_symmetry_vdw_refined	0.163
r_symmetry_hbond_refined	0.159
r_xyhbond_nbd_refined	0.124
r_chiral_restr	0.077
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
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 Atoms	Number
Protein Atoms	1293
Nucleic Acid Atoms
Solvent Atoms	178
Heterogen Atoms	34

Software

Software
Software Name	Purpose
REFMAC	refinement