8QB6 | pdb_00008qb6

Dispersin from Terribacillus saccharophilus DispTs2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other	8QAK	own structure unpublished at the time

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 = 89.688	α = 90
b = 89.688	β = 90
c = 97.685	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-F		2017-06-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

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	1.51	30.4	100	0.056	0.062	0.027	0.999	17.7	10		71635

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)
1	1.51	1.54			1.764	1.966	0.86	0.51		10

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	THROUGHOUT	1.51	30.398	71592	3623	99.98	0.155	0.1534	0.1534	0.1784	0.1785	26.325

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]
-1.493	-0.747		-1.493		4.844

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.936
r_lrange_it	16
r_lrange_other	15.999
r_dihedral_angle_3_deg	13.937
r_dihedral_angle_2_deg	12.817
r_scangle_it	12.638
r_scangle_other	12.635
r_mcangle_it	10.466
r_mcangle_other	10.464
r_scbond_it	9.471
r_scbond_other	9.468
r_mcbond_it	7.956
r_mcbond_other	7.947
r_dihedral_angle_1_deg	6.79
r_rigid_bond_restr	5.339
r_angle_refined_deg	1.593
r_angle_other_deg	0.562
r_nbd_refined	0.228
r_nbd_other	0.21
r_symmetry_nbd_other	0.201
r_nbtor_refined	0.188
r_xyhbond_nbd_refined	0.131
r_symmetry_xyhbond_nbd_refined	0.123
r_symmetry_nbd_refined	0.122
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.081
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2621
Nucleic Acid Atoms
Solvent Atoms	198
Heterogen Atoms	32

Software

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