7Q04 | pdb_00007q04

Crystal structure of TPADO in a substrate-free state

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
2.81	56.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 220.807	α = 90
b = 220.807	β = 90
c = 84.093	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	2.281	110.404	94.3	0.239	0.053	0.998	11	21.1		68994

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	2.281	2.441	63.3		2.767	0.605	0.648	1.4

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	2.281	191.224	68975	3391	64.739	0.181	0.1788	0.18	0.2249	0.23	48.369

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]
0.224	0.112		0.224		-0.727

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.552
r_dihedral_angle_4_deg	17.384
r_dihedral_angle_3_deg	17.376
r_dihedral_angle_1_deg	7.805
r_lrange_other	6.532
r_lrange_it	6.53
r_scangle_it	4.692
r_scangle_other	4.69
r_mcangle_other	4.366
r_mcangle_it	4.365
r_scbond_it	2.923
r_scbond_other	2.921
r_mcbond_it	2.785
r_mcbond_other	2.784
r_angle_refined_deg	1.712
r_angle_other_deg	1.312
r_symmetry_xyhbond_nbd_refined	0.219
r_nbd_other	0.202
r_nbd_refined	0.199
r_symmetry_nbd_other	0.185
r_nbtor_refined	0.165
r_xyhbond_nbd_refined	0.159
r_symmetry_nbd_refined	0.143
r_ncsr_local_group_2	0.103
r_ncsr_local_group_1	0.095
r_ncsr_local_group_4	0.092
r_ncsr_local_group_6	0.092
r_ncsr_local_group_3	0.09
r_metal_ion_refined	0.083
r_symmetry_nbtor_other	0.081
r_ncsr_local_group_5	0.081
r_symmetry_xyhbond_nbd_other	0.077
r_chiral_restr	0.073
r_dihedral_angle_other_3_deg	0.014
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13651
Nucleic Acid Atoms
Solvent Atoms	408
Heterogen Atoms	13

Software

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