6YUT | pdb_00006yut

Structure of recombinant human beta-glucocerebrosidase in complex with N-acyl functionalised cyclophellitol aziridine

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	1 M (NH3)2SO4, 0.17 M guanidine HCl, 0.03 M KCl, 0.1 M sodium acetate pH 4.6

Crystal Properties
Matthews coefficient	Solvent content
3.26	62.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.699	α = 90
b = 285.525	β = 90
c = 91.902	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 X 16M		2016-01-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.979490	Diamond	I02

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	1.76	47.633	99.8	0.098	0.042	0.997	10	6.3		143462

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	1.76	1.79	99.9		0.845	0.37	0.835	1.7	6.2

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	1.76	47.633	143436	7160	99.7	0.184	0.183	0.2	0.2084	0.23	31.049

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]
5.597			-2.895		-2.702

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.051
r_dihedral_angle_4_deg	20.04
r_dihedral_angle_3_deg	13.978
r_dihedral_angle_1_deg	7.202
r_lrange_it	6.016
r_lrange_other	6.016
r_dihedral_angle_other_1_deg	4.82
r_scangle_it	4.192
r_scangle_other	4.192
r_mcangle_it	2.913
r_mcangle_other	2.913
r_scbond_it	2.649
r_scbond_other	2.648
r_mcbond_it	1.931
r_mcbond_other	1.931
r_angle_refined_deg	1.447
r_angle_other_deg	1.267
r_nbd_refined	0.202
r_nbd_other	0.185
r_symmetry_nbd_other	0.182
r_symmetry_nbd_refined	0.179
r_symmetry_xyhbond_nbd_refined	0.169
r_nbtor_refined	0.165
r_xyhbond_nbd_refined	0.162
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.071
r_symmetry_xyhbond_nbd_other	0.055
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7808
Nucleic Acid Atoms
Solvent Atoms	735
Heterogen Atoms	314

Software

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