7YAQ | pdb_00007yaq

Phloem lectin (PP2)C34S mutant

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7VS6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	7.5	295	18% 1,4 butanediol, 300 mM Zinc acetate and 0.1 M Imidazole-HCl pH 6-7

Crystal Properties
Matthews coefficient	Solvent content
2.89	57.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.97	α = 90
b = 51.97	β = 90
c = 261.521	γ = 120

Symmetry
Space Group	P 65 2 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	RIGAKU RAXIS IV		2022-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.85	45.01	98.7	0.21	0.944	6.2	5.7		18583			16.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.95			0.248	0.855	4.3

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	7VUB	1.853	44.395	18583	931	98.136	0.267	0.2643	0.27	0.3162	0.32	18.531

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]
0.129	0.065		0.129		-0.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.234
r_dihedral_angle_3_deg	14.566
r_dihedral_angle_2_deg	7.747
r_dihedral_angle_1_deg	7.664
r_lrange_it	5.04
r_lrange_other	5.021
r_scangle_it	3.672
r_scangle_other	3.67
r_mcangle_other	3.088
r_mcangle_it	3.079
r_scbond_it	2.515
r_scbond_other	2.513
r_mcbond_it	2.122
r_mcbond_other	2.094
r_angle_refined_deg	1.774
r_angle_other_deg	0.982
r_nbd_other	0.306
r_symmetry_nbd_other	0.221
r_nbtor_refined	0.185
r_xyhbond_nbd_refined	0.185
r_nbd_refined	0.182
r_symmetry_xyhbond_nbd_refined	0.167
r_symmetry_nbd_refined	0.165
r_symmetry_nbtor_other	0.09
r_chiral_restr	0.079
r_gen_planes_other	0.015
r_gen_planes_refined	0.011
r_bond_refined_d	0.01
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1220
Nucleic Acid Atoms
Solvent Atoms	67
Heterogen Atoms

Software

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