4GZE | pdb_00004gze

Crystal structure of 6-phospho-beta-glucosidase from Lactobacillus plantarum (apo form)

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	289	0.6 M NaCl, 0.1 M MES/NaOH, 20% PEG4000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.086	α = 90
b = 96.086	β = 90
c = 289.14	γ = 120

Symmetry
Space Group	P 31

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 210r	mirrors	2010-11-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.9794	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	2.31	50	99.6	0.079	21.8	4.4	130885	130353		-3	45.2

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	2.31	2.35	96.7		0.285	2.75	2.8	6313

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 (All)	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	PDB entry 3QOM	2.31	30	130248	130248	1248	99.41	0.17421	0.17421	0.17384	0.17	0.21338	0.21	thin resolution shells	33.569

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]
25.09			25.09		-50.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.38
r_dihedral_angle_4_deg	17.232
r_dihedral_angle_3_deg	14.466
r_dihedral_angle_1_deg	6.422
r_scangle_it	2.19
r_scbond_it	1.497
r_angle_refined_deg	1.309
r_angle_other_deg	0.859
r_mcangle_it	0.805
r_mcbond_it	0.466
r_mcbond_other	0.127
r_chiral_restr	0.082
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	23021
Nucleic Acid Atoms
Solvent Atoms	547
Heterogen Atoms	12

Software

Software
Software Name	Purpose
SBC-Collect	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling