1VKD

Crystal structure of a predicted glycosidase (tm1225) from thermotoga maritima msb8 at 2.10 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP	6.5	293	Cacodylate pH 6.5, 5% PEG-1000, 0.2M MgCl2 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.867	α = 90
b = 100.908	β = 90
c = 253.433	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	CCD	ADSC		2004-02-04	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.115896, 0.979508, 0.979740, 1.019778	ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.098	100.91	91.2	0.086	11.3	4.1		119326			40.37

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.15	78.4		0.521	1.5	2.5	7509

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.1	82.17	113119	6056	91.28	0.16417	0.16203	0.20404	RANDOM	32.363

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]
-0.06			1.62		-1.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.905
r_dihedral_angle_4_deg	20.256
r_dihedral_angle_3_deg	14.538
r_dihedral_angle_1_deg	6.933
r_scangle_it	6.376
r_scbond_it	4.53
r_mcangle_it	2.461
r_mcbond_it	1.532
r_angle_refined_deg	1.418
r_nbd_refined	0.207

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.905
r_dihedral_angle_4_deg	20.256
r_dihedral_angle_3_deg	14.538
r_dihedral_angle_1_deg	6.933
r_scangle_it	6.376
r_scbond_it	4.53
r_mcangle_it	2.461
r_mcbond_it	1.532
r_angle_refined_deg	1.418
r_nbd_refined	0.207
r_symmetry_vdw_refined	0.155
r_xyhbond_nbd_refined	0.138
r_symmetry_hbond_refined	0.134
r_chiral_restr	0.095
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15853
Nucleic Acid Atoms
Solvent Atoms	954
Heterogen Atoms	16

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SOLVE	phasing
SHARP	phasing
autoSHARP	phasing
SOLOMON	phasing
REFMAC	refinement
CCP4	data scaling

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.