3HTD | pdb_00003htd

(Z)-Thiophene-2-carboxaldoxime in complex with T4 lysozyme L99A/M102Q

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1LGU	PDB ENTRY 1LGU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	2.2M sodium-potassium phosphate, 0.05M beta-mercaptoethanol, 0.05M 2-hydroxyethyldisulfide, pH 6.5, vapor diffusion, hanging drop, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.26	α = 90
b = 60.26	β = 90
c = 96.94	γ = 120

Symmetry
Space Group	P 32 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	296	CCD	ADSC QUANTUM 315r		2007-09-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.11589	ALS	8.3.1

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	1.4	30	99.8	0.087	11.36	6.66	40713	40713			20.734

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)
	1.4	1.48	99.7		0.576	2.7	6.22	6131

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	REFMAC	THROUGHOUT	PDB ENTRY 1LGU	1.4	28.77	40712	40712	815	100	0.168	0.168	0.167	0.17	0.19	0.18	RANDOM	15.848

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]
0.44	0.22		0.44		-0.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.02
r_dihedral_angle_3_deg	10.122
r_dihedral_angle_4_deg	10.072
r_dihedral_angle_1_deg	4.488
r_sphericity_free	3.035
r_scangle_it	2.386
r_sphericity_bonded	2.353
r_scbond_it	1.776
r_rigid_bond_restr	1.268
r_angle_refined_deg	1.246
r_mcangle_it	1.126
r_mcbond_it	0.71
r_nbtor_refined	0.307
r_nbd_refined	0.219
r_xyhbond_nbd_refined	0.171
r_symmetry_vdw_refined	0.168
r_symmetry_hbond_refined	0.153
r_chiral_restr	0.073
r_bond_refined_d	0.007
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1387
Nucleic Acid Atoms
Solvent Atoms	331
Heterogen Atoms	29

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction
XDS	data scaling
REFMAC	phasing