4QHZ | pdb_00004qhz

Crystal structure of a putative glycosyl hydrolase (BDI_3914) from Parabacteroides distasonis ATCC 8503 at 2.13 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP, NANODROP		277	0.2M magnesium acetate, 20.0% polyethylene glycol 3350, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.774	α = 90
b = 144.763	β = 101.27
c = 82.452	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M	Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)	2013-11-27	M	MAD
2	1	x-ray	100	CCD	MARMOSAIC 325 mm CCD	double crystal monochromator	2014-02-13	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.97895	SSRL	BL11-1
2	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91837,0.97941	SSRL	BL9-2

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	2.13	48.254	95	0.111	6.96			58318		-3	26.92

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	2.13	2.21	96.6		0.477	2.1

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	2.13	48.254	55339	2948	95.03	0.1724	0.1707	0.18	0.2035	0.21	RANDOM	27.0401

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]
1.21		0.74	-0.3		-0.99

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.614
r_dihedral_angle_3_deg	10.459
r_dihedral_angle_4_deg	8.503
r_dihedral_angle_1_deg	6.98
r_mcangle_it	2.045
r_mcbond_it	1.378
r_mcbond_other	1.378
r_angle_refined_deg	1.199
r_angle_other_deg	0.775
r_chiral_restr	0.041

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.614
r_dihedral_angle_3_deg	10.459
r_dihedral_angle_4_deg	8.503
r_dihedral_angle_1_deg	6.98
r_mcangle_it	2.045
r_mcbond_it	1.378
r_mcbond_other	1.378
r_angle_refined_deg	1.199
r_angle_other_deg	0.775
r_chiral_restr	0.041
r_bond_refined_d	0.006
r_gen_planes_refined	0.004
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7530
Nucleic Acid Atoms
Solvent Atoms	910
Heterogen Atoms	16

Software

Software
Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SOLVE	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	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.