6ZV5

CML1 crystal structure in complex with Lewis a tetrasaccharide

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		292	1.6 M AMSO4, 100 mM trisodium pH 5.6. Crystal flashed freezed in liquid nitrogen after transfer in 2.5 M Li2SO4

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.925	α = 90
b = 73.925	β = 90
c = 119.592	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	PIXEL	DECTRIS EIGER X 16M		2019-07-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.97856	SOLEIL	PROXIMA 1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.95	43.7	98.4	0.056	0.064	0.03	0.999	13	4.3		52412

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2	99.4		0.5	0.575	0.274	0.851		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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6ZU2	1.95	43.7	52408	2590	98.328	0.189	0.1869	0.2392	31.1

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]
-19.854			-19.854		39.707

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.644
r_dihedral_angle_4_deg	16.317
r_dihedral_angle_3_deg	12.002
r_dihedral_angle_1_deg	7.427
r_lrange_it	5.69
r_lrange_other	5.625
r_scangle_it	5.424
r_scangle_other	5.235
r_scbond_it	4.328
r_scbond_other	4.169
r_mcangle_other	4.055
r_mcangle_it	4.051
r_mcbond_it	3.546
r_mcbond_other	3.54
r_angle_refined_deg	1.734
r_angle_other_deg	1.46
r_symmetry_xyhbond_nbd_refined	0.197
r_nbd_other	0.196
r_nbd_refined	0.194
r_symmetry_nbd_other	0.19
r_nbtor_refined	0.17
r_symmetry_nbd_refined	0.166
r_symmetry_xyhbond_nbd_other	0.154
r_xyhbond_nbd_refined	0.15
r_xyhbond_nbd_other	0.121
r_chiral_restr	0.099
r_symmetry_nbtor_other	0.088
r_ncsr_local_group_2	0.07
r_ncsr_local_group_6	0.068
r_ncsr_local_group_8	0.068
r_ncsr_local_group_7	0.066
r_ncsr_local_group_3	0.064
r_ncsr_local_group_9	0.063
r_ncsr_local_group_5	0.062
r_ncsr_local_group_15	0.062
r_ncsr_local_group_4	0.061
r_ncsr_local_group_12	0.061
r_ncsr_local_group_10	0.059
r_ncsr_local_group_11	0.059
r_ncsr_local_group_14	0.059
r_ncsr_local_group_13	0.056
r_ncsr_local_group_1	0.055
r_bond_refined_d	0.015
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5772
Nucleic Acid Atoms
Solvent Atoms	673
Heterogen Atoms	293

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing