6KRN | pdb_00006krn

Crystal structure of GH30 xylanase B from Talaromyces cellulolyticus expressed by Pichia pastoris in complex with aldotriuronic acid

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6IUJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.3	293	PEG 3350, HEPES, magnesium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.251	α = 90
b = 78.7	β = 90
c = 118.418	γ = 90

Symmetry
Space Group	P 21 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	173	PIXEL	DECTRIS EIGER X 16M		2019-06-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.9	SPring-8	BL44XU

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	1.653	33.41	99.41	0.04648	0.05262	0.02424	0.999	15.35	4.5		71087			22.31

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	1.653	1.712	99.03		0.458	0.5184	0.2389	0.847	2.34	4.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	6IUJ	1.653	33.41	71087	3554	99.496	0.171	0.1695	0.18	0.1897	0.2	23.318

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]
1.213			0.101		-1.314

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.378
r_dihedral_angle_4_deg	16.856
r_dihedral_angle_3_deg	12.785
r_dihedral_angle_1_deg	6.222
r_lrange_it	4.876
r_lrange_other	4.77
r_scangle_it	4.262
r_scangle_other	4.261
r_scbond_it	3.257
r_scbond_other	3.257
r_angle_other_deg	3.179
r_mcangle_it	2.892
r_mcangle_other	2.891
r_mcbond_it	2.281
r_mcbond_other	2.281
r_angle_refined_deg	1.704
r_nbd_other	0.223
r_symmetry_nbd_other	0.214
r_nbd_refined	0.21
r_nbtor_refined	0.181
r_symmetry_nbd_refined	0.174
r_symmetry_xyhbond_nbd_refined	0.15
r_xyhbond_nbd_refined	0.123
r_symmetry_nbtor_other	0.115
r_chiral_restr	0.088
r_bond_other_d	0.036
r_bond_refined_d	0.015
r_gen_planes_other	0.006
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3517
Nucleic Acid Atoms
Solvent Atoms	498
Heterogen Atoms	249

Software

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