3HH3 | pdb_00003hh3

New azaborine compounds bind to the T4 lysozyme L99A cavity - 1,2-dihydro-1,2-azaborine

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.9	277	2.0-2.2M K/Na phosphase, 50mM BME, 50mM HED (vapor-diffusion for complex preparation), pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.66	53.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.904	α = 90
b = 59.904	β = 90
c = 95.443	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	100	CCD	ADSC QUANTUM 315	Si(220)	2009-04-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.3	0.9791	ALS	5.0.3

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	1.25	45.58	99.9	0.071	33.6	15.5		55239		5

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)
	1.25	1.27	100		0.269	9.1	10.5	2732

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	3DMV	1.25	45.58	52369	2799	99.65	0.16747	0.16642	0.16	0.18721	0.19	RANDOM	15.635

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]
0.09	0.05		0.09		-0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.233
r_dihedral_angle_3_deg	12.721
r_dihedral_angle_4_deg	9.815
r_dihedral_angle_1_deg	4.92
r_sphericity_free	3.267
r_scangle_it	3.008
r_sphericity_bonded	2.877
r_scbond_it	2.049
r_mcangle_it	1.446
r_rigid_bond_restr	1.216
r_angle_refined_deg	1.172
r_mcbond_it	0.826
r_nbtor_refined	0.306
r_nbd_refined	0.197
r_symmetry_hbond_refined	0.174
r_symmetry_vdw_refined	0.169
r_xyhbond_nbd_refined	0.113
r_chiral_restr	0.072
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_metal_ion_refined	0.002
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_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	1403
Nucleic Acid Atoms
Solvent Atoms	261
Heterogen Atoms	34

Software

Software
Software Name	Purpose
Blu-Ice	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling