1VJZ | pdb_00001vjz

Crystal structure of Endoglucanase (TM1752) from Thermotoga maritima at 2.05 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP	9	277	Bicine pH 9, 2% Dioxane, 10% PEG-20000, pH 9.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
2	VAPOR DIFFUSION,SITTING DROP,NANODROP	9	277	Bicine pH 9, 2% Dioxane, 10% PEG-20000, pH 9.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.684	α = 90
b = 64.684	β = 90
c = 202.189	γ = 90

Symmetry
Space Group	P 43 21 2

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	APS-1	water cooled, sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror	2004-02-20	M	MAD
2	1	x-ray	100	CCD	APS-1	water cooled, sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror	2004-02-20	M	MAD
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM		APS	19-BM
2	SYNCHROTRON	APS BEAMLINE 19-BM	0.964063, 0.979292	APS	19-BM

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
1,2	2.05	50	94.64	0.095	14.57	3.82		26538			34.42

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)
1,2	2.05	2.12	75.23		0.334	3	2.75	2053

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	2.05	32.34	25186	1336	94.87	0.17021	0.16804	0.17	0.21244	0.21	RANDOM	20.751

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]
1.49			1.49		-2.99

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.613
r_dihedral_angle_4_deg	18.087
r_dihedral_angle_3_deg	14.488
r_scangle_it	7.209
r_dihedral_angle_1_deg	6.59
r_scbond_it	5.473
r_mcangle_it	2.967
r_mcbond_it	2.075
r_angle_refined_deg	1.433
r_symmetry_vdw_refined	0.242

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.613
r_dihedral_angle_4_deg	18.087
r_dihedral_angle_3_deg	14.488
r_scangle_it	7.209
r_dihedral_angle_1_deg	6.59
r_scbond_it	5.473
r_mcangle_it	2.967
r_mcbond_it	2.075
r_angle_refined_deg	1.433
r_symmetry_vdw_refined	0.242
r_nbd_refined	0.198
r_symmetry_hbond_refined	0.16
r_xyhbond_nbd_refined	0.159
r_chiral_restr	0.103
r_bond_refined_d	0.016
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2737
Nucleic Acid Atoms
Solvent Atoms	212
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
SOLOMON	phasing
REFMAC	refinement

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.