1NP0 | pdb_00001np0

Human lysosomal beta-hexosaminidase isoform B in complex with intermediate analogue NAG-thiazoline

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	298	5 mg/ml HexB [final], 50% saturated ammonium sulfate, 50 mM potassium phosphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
3.19	61.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 112.414	α = 90
b = 112.414	β = 90
c = 397.232	γ = 120

Symmetry
Space Group	P 61 2 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 4	bent conical Si-mirror (Rh coating)	2001-12-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C	0.9	APS	14-BM-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.5	37					52315		-3

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	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 1NOU	2.5	36.76	49713	2597	100	0.19964	0.1982	0.2	0.22671	0.2	RANDOM	24.379

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]
2.47	1.23		2.47		-3.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.192
r_dihedral_angle_1_deg	4.297
r_scangle_it	2.368
r_angle_refined_deg	1.557
r_scbond_it	1.492
r_angle_other_deg	1.175
r_mcangle_it	0.921
r_nbtor_other	0.48
r_mcbond_it	0.475
r_nbd_refined	0.181
r_xyhbond_nbd_refined	0.152
r_symmetry_vdw_other	0.147
r_symmetry_hbond_refined	0.147
r_nbd_other	0.142
r_symmetry_vdw_refined	0.124
r_chiral_restr	0.092
r_symmetry_hbond_other	0.073
r_xyhbond_nbd_other	0.066
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.003
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7756
Nucleic Acid Atoms
Solvent Atoms	244
Heterogen Atoms	107

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling