9H4T | pdb_00009h4t

Crystal Structure of TorA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DMS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	293	60% PEG 1000, 150 mM di-sodium DL-malate, pH 5.0, 4 mM sodium fluoride

Crystal Properties
Matthews coefficient	Solvent content
2.85	56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.662	α = 90
b = 117.467	β = 103.25
c = 100.053	γ = 90

Symmetry
Space Group	P 1 21 1

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 PILATUS3 S 6M		2018-12-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.9184	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	1.86	47.79	90.88	0.114	0.994	7.45	2.4		159613			22.09

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.86	1.91	88.7		0.543	0.609		2.4

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.86	47.79	157492	2101	90.84	0.2358	0.2351	0.2389	0.28875	0.288	RANDOM	27.921

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]
-0.18		-0.23	2.31		-1.83

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.541
r_long_range_B_refined	8.524
r_long_range_B_other	8.462
r_scangle_other	7.55
r_dihedral_angle_2_deg	7.098
r_dihedral_angle_1_deg	6.706
r_scbond_it	6.018
r_scbond_other	6.018
r_mcangle_it	5.812
r_mcangle_other	5.812
r_mcbond_it	4.837
r_mcbond_other	4.833
r_angle_refined_deg	1.116
r_angle_other_deg	0.421
r_chiral_restr	0.056
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12507
Nucleic Acid Atoms
Solvent Atoms	1544
Heterogen Atoms	424

Software

Software
Software Name	Purpose
REFMAC	refinement
autoXDS	data reduction
XSCALE	data scaling
PHASER	phasing