2D9R

Structure of Conserved Protein of Unknown Function PG0164 from Porphyromonas gingivalis [W83]

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	298	2M NaCl, 0.1M Citric Acid, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.631	α = 90
b = 50.631	β = 90
c = 68.651	γ = 120

Symmetry
Space Group	P 31 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	150	CCD	SBC		2005-07-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.97940	APS	19-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.01	43.85	99.4			6815	6774	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.01	2.08	99.42

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.01	27	2	6815	6774	335	99.65	0.18045	0.1783	0.17829	0.22715	RANDOM	20.94

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]
1.09	0.54		1.09		-1.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_4_deg	24.969
r_dihedral_angle_2_deg	22.839
r_dihedral_angle_3_deg	14.506
r_dihedral_angle_1_deg	13.485
r_scangle_it	4.108
r_scbond_it	2.817
r_angle_refined_deg	1.847
r_mcangle_it	1.72
r_mcbond_it	1.132
r_symmetry_hbond_refined	0.425

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_4_deg	24.969
r_dihedral_angle_2_deg	22.839
r_dihedral_angle_3_deg	14.506
r_dihedral_angle_1_deg	13.485
r_scangle_it	4.108
r_scbond_it	2.817
r_angle_refined_deg	1.847
r_mcangle_it	1.72
r_mcbond_it	1.132
r_symmetry_hbond_refined	0.425
r_symmetry_vdw_refined	0.372
r_nbtor_refined	0.31
r_nbd_refined	0.241
r_xyhbond_nbd_refined	0.185
r_chiral_restr	0.163
r_bond_refined_d	0.017
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	671
Nucleic Acid Atoms
Solvent Atoms	79
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data scaling

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.