2RBO

2-nitrothiophene 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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.1	277	2.2M sodium-potassium phosphate, 0.05M beta-mercaptoethanol, 0.05M 2-hydroxyethyldisulfide, pH 7.1, vapor diffusion, hanging drop, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.107	α = 90
b = 60.107	β = 90
c = 96.715	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	110	CCD	ADSC QUANTUM 315	Vertical focusing mirror; single crystal Si(311) bent monochromator (horizontal focusing)	2006-12-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-1	0.979462	SSRL	BL9-1

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	1.29	52.06	99.9	0.067	11.8	7.6	51583	51583

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)
	1.29	1.34	100		0.622		7.6

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1LGU	1.29	52.06	51537	48915	2622	99.93	0.17433	0.17335	0.19319	RANDOM	14.447

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		-0.06		0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.981
r_dihedral_angle_4_deg	12.315
r_dihedral_angle_3_deg	10.448
r_dihedral_angle_1_deg	4.497
r_sphericity_free	2.434
r_scangle_it	2.089
r_sphericity_bonded	1.969
r_scbond_it	1.684
r_angle_refined_deg	1.216
r_rigid_bond_restr	1.144
r_mcangle_it	0.989
r_mcbond_it	0.631
r_nbtor_refined	0.305
r_nbd_refined	0.192
r_symmetry_vdw_refined	0.137
r_xyhbond_nbd_refined	0.111
r_symmetry_hbond_refined	0.075
r_chiral_restr	0.071
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
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 Atoms	Number
Protein Atoms	1331
Nucleic Acid Atoms
Solvent Atoms	303
Heterogen Atoms	21

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
REFMAC	phasing