7Q05 | pdb_00007q05

Crystal structure of TPADO in complex with 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
2.82	56.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 219.714	α = 90
b = 219.714	β = 90
c = 82.964	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		2021-01-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	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	2.078	190.278	96	0.167	0.037	0.999	14	21.3		111025

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	2.078	2.254	65.5		2.514	0.557	0.667	1.6	21.4

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	2.08	190.278	111023	5502	80.98	0.17	0.1679	0.17	0.214	0.21	46.213

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]
-0.038	-0.019		-0.038		0.122

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.134
r_dihedral_angle_4_deg	18.78
r_dihedral_angle_3_deg	15.199
r_dihedral_angle_1_deg	7.782
r_lrange_it	6.466
r_lrange_other	6.443
r_scangle_it	4.26
r_scangle_other	4.201
r_mcangle_it	3.194
r_mcangle_other	3.194
r_scbond_it	2.988
r_scbond_other	2.94
r_mcbond_it	2.199
r_mcbond_other	2.198
r_angle_refined_deg	1.823
r_angle_other_deg	1.416
r_symmetry_nbd_refined	0.27
r_nbd_other	0.243
r_nbd_refined	0.201
r_symmetry_nbd_other	0.187
r_xyhbond_nbd_refined	0.173
r_nbtor_refined	0.169
r_symmetry_xyhbond_nbd_refined	0.151
r_ncsr_local_group_4	0.102
r_ncsr_local_group_6	0.1
r_ncsr_local_group_2	0.097
r_ncsr_local_group_1	0.089
r_ncsr_local_group_3	0.086
r_ncsr_local_group_5	0.085
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.083
r_symmetry_xyhbond_nbd_other	0.042
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_gen_planes_other	0.004
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13875
Nucleic Acid Atoms
Solvent Atoms	953
Heterogen Atoms	105

Software

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