8VZV | pdb_00008vzv

Human TDO (hTDO) in complex with LM10

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.66	53.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 143.428	α = 90
b = 152.919	β = 90
c = 87.588	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		2017-03-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97931	APS	31-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rpim I (All)	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	2.29	52.31	97.258	0.076	6.6	6.6		85859

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.29	2.41			1.512	0.139

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	2.29	30.002	84922	4274	97.258	0.204	0.2023	0.21	0.2381	0.24	57.005

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]
-0.428			-0.136		0.564

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.366
r_dihedral_angle_3_deg	18.416
r_dihedral_angle_4_deg	16.728
r_lrange_other	11.52
r_lrange_it	11.514
r_scangle_it	8.747
r_scangle_other	8.747
r_mcangle_other	8.459
r_mcangle_it	8.457
r_dihedral_angle_1_deg	5.803
r_scbond_it	5.772
r_scbond_other	5.771
r_mcbond_it	5.659
r_mcbond_other	5.656
r_angle_refined_deg	1.76
r_angle_other_deg	1.298
r_nbd_other	0.295
r_symmetry_nbd_refined	0.249
r_nbd_refined	0.223
r_symmetry_xyhbond_nbd_refined	0.2
r_symmetry_nbd_other	0.179
r_nbtor_refined	0.172
r_xyhbond_nbd_refined	0.167
r_symmetry_xyhbond_nbd_other	0.123
r_ncsr_local_group_4	0.096
r_ncsr_local_group_6	0.094
r_ncsr_local_group_3	0.093
r_ncsr_local_group_2	0.09
r_ncsr_local_group_5	0.09
r_ncsr_local_group_1	0.088
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.075
r_bond_refined_d	0.009
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	11483
Nucleic Acid Atoms
Solvent Atoms	189
Heterogen Atoms	287

Software

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