7LU7 | pdb_00007lu7

Human TDO (hTDO) in complex with NLG919 analog

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6PYZ	PDB entry 6PYZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH		293	50 mM sodium citrate, pH 5.6, 2% Tacsimate, pH 5.0, 5% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 143.263	α = 90
b = 153.811	β = 90
c = 87.975	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	CCD	RAYONIX MX225HE		2017-01-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.979	APS	31-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.299	29.968	99.7	0.998	7.1	1.9		86779

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.34	98.9		0.999		1.7

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	PDB entry 6PYZ	2.3	29.95	86779	4304	99.604	0.192	0.1894	0.19	0.2364	0.24	50.866

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]
-0.299			-1.115		1.415

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.561
r_dihedral_angle_3_deg	17.514
r_dihedral_angle_4_deg	17.34
r_lrange_other	10.841
r_lrange_it	10.837
r_scangle_it	6.692
r_scangle_other	6.692
r_mcangle_other	6.229
r_mcangle_it	6.228
r_dihedral_angle_1_deg	5.41
r_scbond_it	4.233
r_scbond_other	4.233
r_mcbond_it	4.081
r_mcbond_other	4.072
r_angle_refined_deg	1.509
r_angle_other_deg	1.267
r_symmetry_nbd_refined	0.208
r_nbd_refined	0.207
r_nbd_other	0.193
r_symmetry_nbd_other	0.174
r_nbtor_refined	0.17
r_symmetry_xyhbond_nbd_refined	0.165
r_xyhbond_nbd_refined	0.139
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.073
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11364
Nucleic Acid Atoms
Solvent Atoms	397
Heterogen Atoms	320

Software

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