2JFE | pdb_00002jfe

The crystal structure of human cytosolic beta-glucosidase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1V02	PDB ENTRY 1V02

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		CRYSTALS GREW WITHIN SEVERAL DAYS IN THE CRYSTALLIZATION TRIAL CONTAINING 0.2 M AMMONIUM SULPHATE, MES BUFFER AT PH 6.5 AND 30 % (W/V) POLYETHYLENEGLYCOL-MONOMETHYLETHER (PEG-MME) 5500

Crystal Properties
Matthews coefficient	Solvent content
2.82	56.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.479	α = 90
b = 90.479	β = 90
c = 127.925	γ = 120

Symmetry
Space Group	P 31 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 CCD		2005-03-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2		ESRF	ID14-2

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	2.7	45	99.9	0.18	10.6	5.6		17144		1

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	2.7	2.79	100		0.67	3.1	5.7

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1V02	2.7	42.64	16273	865	100	0.201	0.197	0.2	0.28	RANDOM	38.04

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]
1.42	0.71		1.42		-2.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.192
r_dihedral_angle_3_deg	19.646
r_dihedral_angle_4_deg	19.547
r_dihedral_angle_1_deg	8.956
r_scangle_it	2.336
r_angle_refined_deg	1.632
r_scbond_it	1.522
r_mcangle_it	1.097
r_mcbond_it	0.618
r_nbtor_refined	0.318
r_symmetry_hbond_refined	0.261
r_nbd_refined	0.253
r_symmetry_vdw_refined	0.249
r_xyhbond_nbd_refined	0.21
r_chiral_restr	0.12
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
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
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3725
Nucleic Acid Atoms
Solvent Atoms	158
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing