3KST | pdb_00003kst

Crystal structure of Endo-1,4-beta-xylanase (NP_811807.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.70 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.3	277	0.2000M CaAcetate, 20.0000% PEG-3350, No Buffer pH 7.3, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.019	α = 90
b = 90.337	β = 93.82
c = 60.037	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	MARMOSAIC 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2009-03-19	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.89841,0.97915,0.97929	SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.7	28.421	78.3	0.06	9.07			63151		-3	12.066

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.7	1.76	76.6		0.37	2.2

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	MAD	THROUGHOUT	1.7	28.421	63124	3391	89.92	0.147	0.145	0.16	0.179	0.15	THIN SHELL	13.933

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]
-2.6		2	8.56		-5.97

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.077
r_dihedral_angle_4_deg	12.389
r_dihedral_angle_3_deg	11.879
r_dihedral_angle_1_deg	4.934
r_scangle_it	2.493
r_scbond_it	1.748
r_angle_refined_deg	1.746
r_angle_other_deg	1.301
r_mcangle_it	1.102
r_mcbond_it	0.675

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.077
r_dihedral_angle_4_deg	12.389
r_dihedral_angle_3_deg	11.879
r_dihedral_angle_1_deg	4.934
r_scangle_it	2.493
r_scbond_it	1.748
r_angle_refined_deg	1.746
r_angle_other_deg	1.301
r_mcangle_it	1.102
r_mcbond_it	0.675
r_mcbond_other	0.194
r_chiral_restr	0.107
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4745
Nucleic Acid Atoms
Solvent Atoms	514
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction

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.