1S6Y | pdb_00001s6y

2.3A crystal structure of phospho-beta-glucosidase

X-RAY DIFFRACTION

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Crystallization

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.314	α = 90
b = 82.504	β = 90
c = 83.504	γ = 90

Symmetry
Space Group	P 2 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	SBC-3	mirrors	2003-12-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.98080	APS	19-BM

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	2.3	20		0.074		7.2	18209	18209

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	2.3	2.38	82.9		0.343

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	2.31	20	17294	905	94.54	0.19682	0.19403	0.1997	0.25103	0.251	RANDOM	26.437

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]
-1.61			0.16		1.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.686
r_dihedral_angle_3_deg	18.118
r_dihedral_angle_4_deg	17.986
r_dihedral_angle_1_deg	7.945
r_scangle_it	4.656
r_scbond_it	3.229
r_mcangle_it	1.939
r_mcbond_it	1.666
r_angle_refined_deg	1.361
r_angle_other_deg	1.012
r_mcbond_other	0.335
r_symmetry_hbond_refined	0.212
r_nbd_refined	0.202
r_symmetry_vdw_other	0.196
r_nbd_other	0.183
r_symmetry_vdw_refined	0.179
r_xyhbond_nbd_refined	0.169
r_chiral_restr	0.084
r_nbtor_other	0.082
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3223
Nucleic Acid Atoms
Solvent Atoms	140
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing