4S2G | pdb_00004s2g

Joint X-ray/neutron structure of Trichoderma reesei xylanase II at pH 5.8

X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.8	290	PEG8000, 0.1M NaCacodylate, 0.2M NaI, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.514	α = 90
b = 59.872	β = 90
c = 70.431	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	290	IMAGE PLATE	RIGAKU RAXIS IV++	OSMIC VARIMAX	2014-03-12	M	SINGLE WAVELENGTH
2	1	neutron	290	IMAGE PLATE	MAATEL		2013-01-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54
2		OTHER	3.39

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	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	1.6	25.93	96.6	0.075						8.5	3.7		27489
2	2	50	96.2	0.097						11.2	4.7		13899		1.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.66		0.484						1.5	3.6
2	2	2.07		0.327						3.1	3.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	1.6	20			28272	24784	1239	87.7			0.196		0.205		RANDOM	36.81
NEUTRON DIFFRACTION	MOLECULAR REPLACEMENT	2	20			14661	12917	619	88.1			0.164		0.182		RANDOM	36.81

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]

RMS Deviations
Key	Refinement Restraint Deviation
x_dihedral_angle_d	16.6
x_dihedral_angle_d	16.6
x_angle_deg	1.2
x_angle_deg	1.2
x_improper_angle_d	1.14
x_improper_angle_d	1.14
x_bond_d	0.006
x_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1480
Nucleic Acid Atoms
Solvent Atoms	148
Heterogen Atoms	1

Software

Software
Software Name	Purpose
nCNS	refinement
HKL-3000	data collection
DENZO	data reduction
HKL-3000	data reduction
SCALEPACK	data scaling
CNS	phasing

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.