7Q06 | pdb_00007q06

Crystal structure of TPADO in complex with 2-OH-TPA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3N0Q	3N0Q, 3EBY
experimental model	PDB	3EBY	3N0Q, 3EBY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	12.5% MPD, 12.5% PEG 3350, 12.5% PEG 1000, 0.3 M sodium nitrate, 0.3 M sodium phosphate dibasic, 0.3 M ammonium sulfate, 0.1 M buffer Imidazole/MES pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.85	56.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 220.312	α = 90
b = 220.312	β = 90
c = 83.175	γ = 120

Symmetry
Space Group	P 61

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 EIGER2 XE 16M		2021-07-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

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	1.948	190.796	96.4	0.109	0.027	0.999	17.9	17.3		149913

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	1.948	2.057	57.4		2.372	0.56	0.59	1.4	18.5

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	FREE R-VALUE	3N0Q, 3EBY	1.95	190.796	149903	7226	89.47	0.167	0.1648	0.17	0.2022	0.21	43.123

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]
0.027	0.014		0.027		-0.089

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.374
r_dihedral_angle_4_deg	17.993
r_dihedral_angle_3_deg	14.079
r_dihedral_angle_1_deg	7.482
r_lrange_it	7.052
r_lrange_other	7.046
r_scangle_other	5.378
r_scangle_it	5.377
r_mcangle_it	3.94
r_mcangle_other	3.94
r_scbond_it	3.776
r_scbond_other	3.772
r_mcbond_it	2.835
r_mcbond_other	2.835
r_angle_refined_deg	1.814
r_angle_other_deg	1.449
r_nbd_other	0.243
r_symmetry_nbd_refined	0.235
r_symmetry_xyhbond_nbd_other	0.206
r_nbd_refined	0.201
r_symmetry_nbd_other	0.184
r_symmetry_xyhbond_nbd_refined	0.171
r_nbtor_refined	0.169
r_xyhbond_nbd_refined	0.152
r_ncsr_local_group_4	0.103
r_ncsr_local_group_2	0.1
r_ncsr_local_group_6	0.099
r_ncsr_local_group_1	0.098
r_ncsr_local_group_5	0.087
r_chiral_restr	0.085
r_symmetry_nbtor_other	0.082
r_ncsr_local_group_3	0.079
r_bond_refined_d	0.014
r_xyhbond_nbd_other	0.011
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13861
Nucleic Acid Atoms
Solvent Atoms	921
Heterogen Atoms	83

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
STARANISO	data scaling
MOLREP	phasing