4S2H | pdb_00004s2h

Joint X-ray/neutron structure of Trichoderma reesei xylanase II at pH 8.5

X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	275	PEG8000, 0.1M TRIS, 0.2M NaI, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 275.0K

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.613	α = 90
b = 60.033	β = 90
c = 70.553	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	291	IMAGE PLATE	RIGAKU RAXIS IV++	OSMIC VARIMAX	2010-06-25	M	SINGLE WAVELENGTH
2	1	neutron	291	AREA DETECTOR	3He PSD		2010-08-09	M

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54
2	NUCLEAR REACTOR	OTHER	0.7-7.0

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	1.55	33.62	96.8	0.069						9.8	4.2		30268
2	1.7	22.86	85.3	0.237						5.1	3.3		20012		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	1.55	1.61		0.449						1.9	3.98
2	1.7	1.79		0.364						1.7	2

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	19.25			28453	25612	1263	90			0.199		0.21		RANDOM	26.4
NEUTRON DIFFRACTION	MOLECULAR REPLACEMENT	1.7	19.25			23810	17268	823	72.5			0.261		0.268		RANDOM	26.4

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	16.8
x_dihedral_angle_d	16.8
x_angle_deg	1.2
x_angle_deg	1.2
x_improper_angle_d	1.05
x_improper_angle_d	1.05
x_bond_d	0.011
x_bond_d	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1480
Nucleic Acid Atoms
Solvent Atoms	170
Heterogen Atoms	1

Software

Software
Software Name	Purpose
nCNS	refinement
HKL-2000	data collection
d*TREK	data scaling
HKL-2000	data reduction
d*TREK	data reduction
LAUENORM	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.