4RDB | pdb_00004rdb

Crystal structure of an immunoreactive 32 kDa antigen PG49 (PG_0181) from Porphyromonas gingivalis W83 at 1.45 A resolution (PSI Community Target, Nakayama)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9	293	0.17M sodium acetate, 15.0% Glycerol, 28.5% polyethylene glycol 4000, 4.0% Acetone, 0.1M TRIS pH 9.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.636	α = 90
b = 86.821	β = 90
c = 90.645	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	PIXEL	DECTRIS PILATUS 6M	Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator	2014-07-28	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.9184,0.9791	SSRL	BL12-2

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	1.45	43.411	99.1	0.083	13.38			55908		-3	11.182

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	1.45	1.5	98.3		0.714	2.3

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	1.45	43.411	55846	2833	99.14	0.1191	0.1171	0.13	0.1569	0.16	RANDOM	15.1539

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]
0.38			0.39		-0.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.035
r_sphericity_free	29.418
r_dihedral_angle_4_deg	17.957
r_rigid_bond_restr	11.703
r_dihedral_angle_3_deg	10.897
r_sphericity_bonded	9.542
r_dihedral_angle_1_deg	6.415
r_mcangle_it	1.975
r_mcbond_it	1.729
r_mcbond_other	1.728

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.035
r_sphericity_free	29.418
r_dihedral_angle_4_deg	17.957
r_rigid_bond_restr	11.703
r_dihedral_angle_3_deg	10.897
r_sphericity_bonded	9.542
r_dihedral_angle_1_deg	6.415
r_mcangle_it	1.975
r_mcbond_it	1.729
r_mcbond_other	1.728
r_angle_refined_deg	1.605
r_angle_other_deg	0.779
r_chiral_restr	0.096
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2383
Nucleic Acid Atoms
Solvent Atoms	420
Heterogen Atoms	56

Software

Software
Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
REFMAC	refinement
XDS	data reduction
SHELXD	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.