9I9H | pdb_00009i9h

Structure of FAB-fragment GB11 in complex with Sialyl Lewis A

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6XTG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		292	sodium malonate PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.51	51.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.838	α = 89.602
b = 108.697	β = 87.339
c = 108.92	γ = 89.251

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 PILATUS 2M		2021-12-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.9184	BESSY	14.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.9	26.98	98.2	0.407	0.222	0.915	2.8	3		40947			49.14

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.9	3.02			2.583	1.359	0.189	0.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.96	26.696	37583	1994	98.697	0.212	0.2097	0.2166	0.2479	0.2552	61.588

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]
2.256	-1.535	0.416	0.204	0.366	-2.447

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.574
r_lrange_it	13.77
r_lrange_other	13.77
r_dihedral_angle_6_deg	12.744
r_mcangle_it	8.594
r_mcangle_other	8.594
r_scangle_it	8.284
r_scangle_other	8.284
r_dihedral_angle_1_deg	7.814
r_dihedral_angle_2_deg	6.989
r_mcbond_it	5.303
r_mcbond_other	5.302
r_scbond_it	5.015
r_scbond_other	5.015
r_angle_refined_deg	1.321
r_angle_other_deg	0.741
r_symmetry_xyhbond_nbd_refined	0.341
r_nbd_other	0.271
r_xyhbond_nbd_refined	0.259
r_nbd_refined	0.252
r_symmetry_nbd_other	0.232
r_symmetry_nbd_refined	0.212
r_nbtor_refined	0.179
r_ncsr_local_group_3	0.15
r_ncsr_local_group_11	0.148
r_ncsr_local_group_12	0.148
r_xyhbond_nbd_other	0.132
r_ncsr_local_group_2	0.099
r_ncsr_local_group_1	0.098
r_ncsr_local_group_9	0.096
r_ncsr_local_group_8	0.091
r_symmetry_nbtor_other	0.089
r_ncsr_local_group_5	0.088
r_ncsr_local_group_7	0.088
r_ncsr_local_group_10	0.088
r_ncsr_local_group_4	0.085
r_ncsr_local_group_6	0.083
r_symmetry_xyhbond_nbd_other	0.075
r_chiral_restr	0.06
r_ext_dist_refined_b	0.01
r_gen_planes_other	0.006
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13216
Nucleic Acid Atoms
Solvent Atoms	18
Heterogen Atoms	259

Software

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