3GYC | pdb_00003gyc

Crystal structure of putative glycoside hydrolase (YP_001304622.1) from Parabacteroides distasonis ATCC 8503 at 1.85 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	277	NANODROP, 20.0% PEG 3000, 0.1M Citrate pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.12	42.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.209	α = 90
b = 84.915	β = 94.25
c = 77.991	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	CCD	MARMOSAIC 325 mm CCD	Flat mirror, vertical and horizontal focusing mirrors	2009-01-29	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.91162, 0.97954	SSRL	BL12-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.85	29.604	100	0.093	0.093	9.4	3.8		66845			22.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.9	100		0.67	0.67	1.9	3.8	4946

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	1.85	29.604	66817	3384	99.97	0.171	0.169	0.19	0.205	0.21	RANDOM	16.106

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]
0.29		-1.03	1.67		-2.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.483
r_dihedral_angle_4_deg	15.85
r_dihedral_angle_3_deg	12.338
r_dihedral_angle_1_deg	4.085
r_scangle_it	1.997
r_mcangle_it	1.704
r_angle_refined_deg	1.557
r_scbond_it	1.354
r_mcbond_it	1.085
r_angle_other_deg	0.966

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.483
r_dihedral_angle_4_deg	15.85
r_dihedral_angle_3_deg	12.338
r_dihedral_angle_1_deg	4.085
r_scangle_it	1.997
r_mcangle_it	1.704
r_angle_refined_deg	1.557
r_scbond_it	1.354
r_mcbond_it	1.085
r_angle_other_deg	0.966
r_mcbond_other	0.303
r_chiral_restr	0.106
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6269
Nucleic Acid Atoms
Solvent Atoms	415
Heterogen Atoms	24

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	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.