8R75 | pdb_00008r75

Polysaccharide lyase BtPL33HA (BT4410) Apo form 1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	RoseTTAFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295	20 % PEG 3350 0.2 M Na/K Tartrate 20 mg/ml protein

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.37	α = 90
b = 101.58	β = 90
c = 161.83	γ = 90

Symmetry
Space Group	P 2 21 21

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 EIGER X 16M		2019-04-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	1.6533	Diamond	I04

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	2.7	48.61	100	0.999	15.8	31.4		34414

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	2.7	2.83			0.735	1.3

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	2.7	48.506	34414	1694	99.922	0.185	0.18	0.1803	0.2782	0.2794	90.08

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]
-1.139			-3.339		4.478

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.821
r_dihedral_angle_6_deg	15.166
r_lrange_other	12.717
r_lrange_it	12.716
r_scangle_it	11.262
r_scangle_other	11.261
r_mcangle_other	9.91
r_mcangle_it	9.909
r_dihedral_angle_2_deg	9.802
r_scbond_it	8.345
r_scbond_other	8.345
r_dihedral_angle_1_deg	7.828
r_mcbond_it	7.486
r_mcbond_other	7.486
r_angle_refined_deg	2.1
r_angle_other_deg	0.691
r_nbd_refined	0.23
r_symmetry_nbd_other	0.204
r_nbd_other	0.196
r_symmetry_nbd_refined	0.195
r_nbtor_refined	0.193
r_xyhbond_nbd_refined	0.185
r_symmetry_xyhbond_nbd_refined	0.174
r_symmetry_xyhbond_nbd_other	0.102
r_ncsr_local_group_1	0.099
r_chiral_restr	0.097
r_metal_ion_refined	0.09
r_symmetry_nbtor_other	0.087
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9885
Nucleic Acid Atoms
Solvent Atoms	2
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing