6KRL | pdb_00006krl

Crystal structure of GH30 xylanase B from Talaromyces cellulolyticus expressed by Pichia pastoris

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	7.5	293	PEG 3350, HEPES, magnesium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.337	α = 90
b = 78.765	β = 90
c = 117.839	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	100	PIXEL	DECTRIS EIGER X 16M		2019-01-24	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)	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	1.601	43.144	99.59	0.09292	0.03888	0.996	11.8	6.7		78001			21.05

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.601	1.658	96.61		0.8014	0.3322	0.66	2	6.8

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	1.601	43.14	78001	3900	99.602	0.174	0.1723	0.18	0.1984	0.21	22.058

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]
0.521			0.119		-0.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.739
r_dihedral_angle_4_deg	17.278
r_dihedral_angle_3_deg	11.781
r_dihedral_angle_1_deg	6.712
r_lrange_it	4.717
r_lrange_other	4.574
r_scangle_it	3.228
r_scangle_other	3.228
r_mcangle_other	2.282
r_mcangle_it	2.281
r_scbond_it	2.091
r_scbond_other	2.091
r_angle_refined_deg	1.483
r_mcbond_it	1.452
r_mcbond_other	1.448
r_angle_other_deg	1.431
r_nbd_refined	0.199
r_symmetry_nbd_other	0.18
r_symmetry_xyhbond_nbd_refined	0.175
r_nbtor_refined	0.167
r_nbd_other	0.152
r_xyhbond_nbd_refined	0.127
r_symmetry_nbtor_other	0.113
r_chiral_restr	0.07
r_symmetry_nbd_refined	0.058
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3500
Nucleic Acid Atoms
Solvent Atoms	410
Heterogen Atoms	187

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data scaling
MOLREP	phasing
Coot	model building
XDS	data reduction