5BMT

Crystal structure of an uncharacterized protein (PARMER_03598) from Parabacteroides merdae ATCC 43184 at 1.50 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	10.5	277	0.2M lithium sulfate, 2.0M ammonium sulfate, 0.1M CAPS pH 10.5

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.75	α = 90
b = 58.969	β = 90
c = 165.462	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	MARMOSAIC 325 mm CCD	Vertical focusing mirror; double crystal Si(111) monochromator	2014-12-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL14-1	0.97951	SSRL	BL14-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (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	1.5	29.212	99.8	0.059	0.069	12.12	3.796		91355		-3	18.883

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.55	99.3		0.8	0.936	1.8

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	SAD	THROUGHOUT	1.5	29.212	91266	4569	99.95	0.1671	0.1661	0.1861	RANDOM	25.2128

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]
0.5691			-0.7371		0.168

RMS Deviations
Key	Refinement Restraint Deviation
t_omega_torsion	4.72
t_other_torsion	2.36
t_angle_deg	1.06
t_bond_d	0.01
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion

RMS Deviations
Key	Refinement Restraint Deviation
t_omega_torsion	4.72
t_other_torsion	2.36
t_angle_deg	1.06
t_bond_d	0.01
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_pseud_angle
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3529
Nucleic Acid Atoms
Solvent Atoms	697
Heterogen Atoms	86

Software

Software
Software Name	Purpose
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XDS	data reduction
XSCALE	data scaling
BUSTER	refinement
SHELXD	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.