6Z39 | pdb_00006z39

Structure of recombinant human beta-glucocerebrosidase in complex with BODIPY functionalised epoxide activity based probe

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2NT0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	0.95 M (NH3)2SO4, 0.17 M guanidine HCl, 0.02 M KCl, 0.1 M sodium acetate pH 4.6

Crystal Properties
Matthews coefficient	Solvent content
3.27	62.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.172	α = 90
b = 285.622	β = 90
c = 91.564	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER2 XE 16M		2015-12-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.976300	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	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	1.7	103.82	100	0.09	0.04	0.999	13.3	6		159511

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.73			0.973	0.445	0.761	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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2NT0	1.7	103.816	159484	7997	99.91	0.163	0.1626	0.17	0.1805	0.19	23.297

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]
3.633			-1.26		-2.373

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.952
r_dihedral_angle_4_deg	19.31
r_dihedral_angle_3_deg	13.101
r_dihedral_angle_1_deg	7.269
r_lrange_it	4.892
r_lrange_other	4.892
r_dihedral_angle_other_1_deg	3.541
r_scangle_it	2.943
r_scangle_other	2.943
r_mcangle_it	1.886
r_mcangle_other	1.886
r_scbond_it	1.833
r_scbond_other	1.833
r_angle_refined_deg	1.434
r_angle_other_deg	1.288
r_mcbond_it	1.186
r_mcbond_other	1.185
r_dihedral_angle_other_2_deg	0.803
r_symmetry_nbd_refined	0.202
r_nbd_refined	0.197
r_symmetry_nbd_other	0.174
r_nbd_other	0.168
r_nbtor_refined	0.163
r_symmetry_xyhbond_nbd_refined	0.159
r_symmetry_xyhbond_nbd_other	0.15
r_xyhbond_nbd_refined	0.148
r_chiral_restr	0.095
r_symmetry_nbtor_other	0.076
r_bond_refined_d	0.006
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	7840
Nucleic Acid Atoms
Solvent Atoms	904
Heterogen Atoms	331

Software

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