Experiment: 9O5H

Crystal structure of GH30_8 xylanase from Bacillus pumilus

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3GTN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291.15	20% (w/v) PEG 3350 and 0.18 M ammonium citrate

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.084	α = 90
b = 101.484	β = 90
c = 158.689	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 PILATUS 2M		2022-03-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS SIRIUS BEAMLINE MANACA	0.977	LNLS SIRIUS	MANACA

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	2.16	48.65	98.54	0.996	8.58	2		51299			35.06

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	2.16	2.237			0.489

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.16	48.65	48736	2567	98.5	0.1934	0.19224	0.2004	0.21547	0.2273	RANDOM	39.817

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]
-0.23			-1		1.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.688
r_long_range_B_refined	5.939
r_long_range_B_other	5.913
r_dihedral_angle_1_deg	5.744
r_scangle_other	4.627
r_mcangle_it	3.226
r_mcangle_other	3.226
r_scbond_it	2.952
r_scbond_other	2.952
r_mcbond_it	2.129

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.688
r_long_range_B_refined	5.939
r_long_range_B_other	5.913
r_dihedral_angle_1_deg	5.744
r_scangle_other	4.627
r_mcangle_it	3.226
r_mcangle_other	3.226
r_scbond_it	2.952
r_scbond_other	2.952
r_mcbond_it	2.129
r_mcbond_other	2.129
r_angle_refined_deg	0.837
r_angle_other_deg	0.322
r_chiral_restr	0.044
r_bond_refined_d	0.004
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6230
Nucleic Acid Atoms
Solvent Atoms	251
Heterogen Atoms	37

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
XSCALE	data scaling
PHASER	phasing

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.