7DED | pdb_00007ded

Mevo lectin complex with mannoheptose (Man7)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7BSB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	6	295	Tacsimate pH 6.0, 0.1 M MES monohydrate pH 6.0, 25 % (w/v) PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
3.49	59.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 168.35	α = 90
b = 168.35	β = 90
c = 104.96	γ = 90

Symmetry
Space Group	P 42 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR scanner 345 mm plate		2020-04-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.54

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	2.22	61.18	99.7	0.39	0.091	0.985	7.8	19.2		73523			16.6

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	2.23	2.35	98		0.813	0.196	0.524	3.2	17.6

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	THROUGHOUT	7BSB	2.228	59.592	73482	3622	99.383	0.248	0.2465	0.25	0.2667	0.27	19.837

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]
-1.494			-1.494		2.988

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.082
r_dihedral_angle_3_deg	14.75
r_dihedral_angle_4_deg	9.407
r_dihedral_angle_1_deg	8.597
r_lrange_it	5.588
r_lrange_other	5.588
r_scangle_it	3.972
r_scangle_other	3.972
r_mcangle_it	3.837
r_mcangle_other	3.837
r_scbond_it	2.542
r_scbond_other	2.542
r_angle_other_deg	2.405
r_mcbond_it	2.355
r_mcbond_other	2.355
r_angle_refined_deg	1.689
r_nbd_other	0.222
r_symmetry_nbd_other	0.215
r_nbd_refined	0.175
r_nbtor_refined	0.168
r_symmetry_xyhbond_nbd_refined	0.167
r_xyhbond_nbd_refined	0.153
r_symmetry_nbd_refined	0.124
r_symmetry_xyhbond_nbd_other	0.094
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.066
r_bond_other_d	0.036
r_gen_planes_other	0.02
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_chiral_restr_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7427
Nucleic Acid Atoms
Solvent Atoms	127
Heterogen Atoms	273

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing