5FOO | pdb_00005foo

6-phospho-beta-glucosidase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4B3K	PDB ENTRY 4B3K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		0.33 MM SPY1599 WAS REACTED WITH 4.2 MM 6-PHOSPHO-CYCLOPHELLITOL EPOXIDE IN THE BUFFER OF 50 MM HEPES AND 150 MM NACL, PH 7.0, BEFORE BEING MIXED WITH THE SAME VOLUME OF BUFFER OF 0.1 M BIS TRIS PROPANE PH7.5, 20% PEG 3350 AND 0.15 M NABR

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.017	α = 90
b = 109.899	β = 92.02
c = 158.5	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	PIXEL	DECTRIS PILATUS 6M		2014-04-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04		Diamond	I04

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	2.1	49.47	99.9	0.07	12.6	4.2		205534		1.9

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	2.1	2.14	99.9		0.62	1.9	4.2

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	PDB ENTRY 4B3K	2.1	158.4	195049	10459	99.91	0.17625	0.17385	0.18	0.21989	0.22	RANDOM	36.306

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]
0.99		-0.15	0.43		-1.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.726
r_dihedral_angle_4_deg	17.969
r_dihedral_angle_3_deg	14.118
r_dihedral_angle_1_deg	10.899
r_mcangle_it	3.755
r_scbond_it	3.628
r_mcbond_it	2.891
r_mcbond_other	2.889
r_angle_refined_deg	1.843
r_angle_other_deg	1.116
r_chiral_restr	0.111
r_bond_refined_d	0.018
r_gen_planes_refined	0.011
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_it
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	22644
Nucleic Acid Atoms
Solvent Atoms	981
Heterogen Atoms	213

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
MOLREP	phasing