9GV3 | pdb_00009gv3

Crystal structure of the complex between Nb474 mutant R53A,D125A and Trypanosoma congolense fructose-1,6-bisphosphate aldolase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5O0W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	sodium cacodylate pH 6.5, 100mM, PEG 8K 10-15%, 200mM magnesium acetate.

Crystal Properties
Matthews coefficient	Solvent content
2.98	58.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 203.495	α = 90
b = 111.166	β = 90
c = 123.244	γ = 90

Symmetry
Space Group	P 21 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	PIXEL	DECTRIS PILATUS 6M		2022-07-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.6702	Diamond	I24

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	1.75	97.558	87.6	0.117	0.135	0.055	0.998	9.2	5.1		999301

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	1.751	1.915	64.8		1.058	0.525	0.533	1.6	4.4

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	1.751	97.558	197213	9820	70.488	0.161	0.1598	0.1597	0.1882	0.1882	32.24

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]
-0.241			0.166		0.075

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.33
r_dihedral_angle_3_deg	13.299
r_dihedral_angle_2_deg	8.76
r_lrange_it	7.91
r_scangle_it	6.628
r_dihedral_angle_1_deg	6.575
r_scbond_it	4.874
r_mcangle_it	3.672
r_mcbond_it	2.635
r_angle_refined_deg	2.224
r_nbtor_refined	0.311
r_symmetry_xyhbond_nbd_refined	0.236
r_nbd_refined	0.213
r_symmetry_nbd_refined	0.191
r_xyhbond_nbd_refined	0.159
r_chiral_restr	0.142
r_ncsr_local_group_12	0.11
r_ncsr_local_group_9	0.095
r_ncsr_local_group_11	0.094
r_ncsr_local_group_7	0.076
r_ncsr_local_group_10	0.076
r_ncsr_local_group_8	0.066
r_ncsr_local_group_3	0.059
r_ncsr_local_group_2	0.057
r_ncsr_local_group_6	0.057
r_ncsr_local_group_1	0.055
r_ncsr_local_group_4	0.054
r_ncsr_local_group_5	0.049
r_bond_refined_d	0.015
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15243
Nucleic Acid Atoms
Solvent Atoms	1343
Heterogen Atoms	22

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
STARANISO	data scaling
PHASER	phasing