7VUB | pdb_00007vub

Phloem lectin (PP2) complex with Nitrobenzene

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		295	1.0 M Ammonium citrate dibasic, 0.1 M Sodium acetate trihydrate pH 4.6

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.81	α = 90
b = 70.47	β = 90
c = 101.95	γ = 90

Symmetry
Space Group	P 21 21 21

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 6M		2020-03-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	1.0	ELETTRA	11.2C

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	1.2	50.97	100	0.073	1	2.5	26.6		2585878			11.7

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	1.2	1.22			1.27	0.85

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	7VS6	1.2	50.9	97099	4765	99.971	0.162	0.1603	0.17	0.1893	0.19	16.129

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]
-2.676			1.756		0.92

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.484
r_rigid_bond_restr	29.728
r_dihedral_angle_4_deg	17.029
r_dihedral_angle_3_deg	10.032
r_dihedral_angle_1_deg	7.225
r_scbond_other	5.01
r_scbond_it	5.008
r_scangle_it	4.338
r_scangle_other	4.336
r_lrange_it	3.955
r_lrange_other	3.914
r_mcangle_it	3.036
r_mcangle_other	3.035
r_mcbond_it	2.844
r_mcbond_other	2.841
r_angle_other_deg	2.401
r_angle_refined_deg	2.026
r_symmetry_nbd_other	0.221
r_symmetry_xyhbond_nbd_refined	0.197
r_nbd_refined	0.185
r_nbtor_refined	0.181
r_symmetry_nbd_refined	0.17
r_nbd_other	0.128
r_chiral_restr	0.113
r_xyhbond_nbd_refined	0.112
r_ncsr_local_group_1	0.093
r_symmetry_nbtor_other	0.088
r_symmetry_xyhbond_nbd_other	0.044
r_gen_planes_other	0.037
r_bond_other_d	0.036
r_bond_refined_d	0.018
r_gen_planes_refined	0.016

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2413
Nucleic Acid Atoms
Solvent Atoms	362
Heterogen Atoms	13

Software

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