8B48

Structure of Lentithecium fluviatile carbohydrate esterase from the CE15 family (LfCE15C)

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277.15	Protein stock: 13.7 mg/mL in 20 mM Tris pH 8.0 Reservoir: 0.2 M Ammonium formate pH 6.6, 20 %w/v PEG 3350 Drop: 3:1 protein to reservoir ratio

Crystal Properties
Matthews coefficient	Solvent content
2.51	51.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.74	α = 113.322
b = 79.57	β = 98.531
c = 86.01	γ = 94.44

Symmetry
Space Group	P 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	PIXEL	DECTRIS EIGER X 16M		2018-06-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.980779	MAX IV	BioMAX

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.65	47.254	97.4	0.982	4.3	3.8		47781

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.65	2.72	97.2		0.513	1	3.9

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3PIC	2.65	47.254	47781	2294	97.626	0.241	0.2379	0.2977	59.101

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]
4.938	-2.676	5.124	-2.868	-2.909	-0.623

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.509
r_dihedral_angle_4_deg	18.085
r_dihedral_angle_3_deg	17.73
r_dihedral_angle_other_3_deg	13.788
r_lrange_it	11.823
r_lrange_other	11.821
r_dihedral_angle_1_deg	7.225
r_scangle_it	7.042
r_scangle_other	7.041
r_mcangle_it	6.859
r_mcangle_other	6.858
r_scbond_it	4.583
r_scbond_other	4.583
r_mcbond_it	4.419
r_mcbond_other	4.418
r_angle_refined_deg	1.448
r_angle_other_deg	1.183
r_nbd_other	0.28
r_symmetry_nbd_refined	0.203
r_nbd_refined	0.199
r_symmetry_xyhbond_nbd_refined	0.193
r_symmetry_nbd_other	0.187
r_xyhbond_nbd_refined	0.169
r_nbtor_refined	0.164
r_symmetry_xyhbond_nbd_other	0.091
r_symmetry_nbtor_other	0.085
r_ncsr_local_group_1	0.07
r_ncsr_local_group_5	0.066
r_ncsr_local_group_4	0.064
r_ncsr_local_group_2	0.06
r_chiral_restr	0.057
r_ncsr_local_group_3	0.055
r_ncsr_local_group_6	0.046
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11382
Nucleic Acid Atoms
Solvent Atoms	303
Heterogen Atoms	250

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing