9HTA | pdb_00009hta

Dispersin from Terribacillus saccharophilus Dispts2 in complex with NAG-thiazoline

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8QB6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	MPD screen E7: 0.1 M Citric acid pH 4.0, 20% MPD

Crystal Properties
Matthews coefficient	Solvent content
3.02	59.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.06	α = 90
b = 90.06	β = 90
c = 98.12	γ = 120

Symmetry
Space Group	P 32 2 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 PILATUS 6M		2018-03-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.976	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.17	40.93	93.1	0.09	0.099	0.04	0.999	13.3	11.6		23157

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.17	2.24	76.4		4.735	5.21	2.151	0.532	0.5	11.2

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	2.17	40.926	23065	1089	92.895	0.214	0.2121	0.2122	0.2528	0.2527	59.004

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]
0.595	0.298		0.595		-1.93

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.536
r_dihedral_angle_3_deg	13.6
r_lrange_it	9.215
r_lrange_other	9.215
r_dihedral_angle_2_deg	7.533
r_dihedral_angle_1_deg	6.994
r_scangle_it	6.978
r_scangle_other	6.976
r_mcangle_it	6.432
r_mcangle_other	6.43
r_mcbond_it	4.642
r_mcbond_other	4.641
r_scbond_it	4.568
r_scbond_other	4.564
r_angle_refined_deg	1.482
r_angle_other_deg	0.564
r_nbd_refined	0.207
r_nbtor_refined	0.182
r_symmetry_nbd_other	0.176
r_nbd_other	0.146
r_xyhbond_nbd_refined	0.128
r_symmetry_xyhbond_nbd_refined	0.103
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.069
r_symmetry_nbd_refined	0.051
r_gen_planes_refined	0.006
r_bond_refined_d	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2631
Nucleic Acid Atoms
Solvent Atoms	43
Heterogen Atoms	14

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
Aimless	data scaling
MOLREP	phasing