3KS7 | pdb_00003ks7

Crystal structure of Putative Peptide:N-glycosidase F (PNGase F) (YP_210507.1) from Bacteroides fragilis NCTC 9343 at 2.30 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	25.0000% polyethylene glycol 3350, 0.2070M ammonium iodide, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.73	54.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.057	α = 90
b = 119.221	β = 90
c = 154.314	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	Flat mirror (vertical focusing)	2009-07-08	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837,0.97922,0.97876	SSRL	BL11-1

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	2.3	29.881	99.8	0.099	0.099	9.9	3.7		87284			43.391

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	2.3	2.36	99.9		0.789	0.789	1	3.8	6398

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	2.3	29.881	87221	4375	99.74	0.203	0.201	0.2	0.237	0.23	RANDOM	26.071

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]
2.57			-0.86		-1.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.277
r_dihedral_angle_4_deg	19.274
r_dihedral_angle_3_deg	11.251
r_dihedral_angle_1_deg	4.828
r_scangle_it	1.844
r_scbond_it	1.128
r_angle_refined_deg	1.052
r_mcangle_it	0.806
r_angle_other_deg	0.667
r_mcbond_it	0.421

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.277
r_dihedral_angle_4_deg	19.274
r_dihedral_angle_3_deg	11.251
r_dihedral_angle_1_deg	4.828
r_scangle_it	1.844
r_scbond_it	1.128
r_angle_refined_deg	1.052
r_mcangle_it	0.806
r_angle_other_deg	0.667
r_mcbond_it	0.421
r_mcbond_other	0.073
r_chiral_restr	0.061
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12201
Nucleic Acid Atoms
Solvent Atoms	456
Heterogen Atoms	105

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
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.