2P3P

Structure of a domain of an uncharacterized protein PG_1388 from Porphyromonas gingivalis W83

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	291	0.2M Ammonium acetate, 0.1M BIS-TRIS pH 6.5, 25 % w/v PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.2	43.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.753	α = 86.55
b = 48.259	β = 79.58
c = 54.191	γ = 68.35

Symmetry
Space Group	P 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	ADSC QUANTUM 315	mirrors	2007-02-05	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97924, 0.97938	APS	19-ID

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	1.76	35	92.9	0.07	14.4	3.5	37374	37374			27.2

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	1.76	1.79	71.7		0.19	6	3.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.76	35	35455	35455	1873	92.89	0.16849	0.16547	0.22645	RANDOM	9.885

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]
0.56	-0.27	-0.38	0.33	0.41	-0.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.31
r_dihedral_angle_4_deg	20.251
r_dihedral_angle_3_deg	12.458
r_dihedral_angle_1_deg	6.187
r_scangle_it	2.784
r_scbond_it	2.049
r_angle_refined_deg	1.566
r_mcangle_it	1.195
r_angle_other_deg	0.936
r_mcbond_it	0.93
r_symmetry_vdw_other	0.282
r_mcbond_other	0.26
r_symmetry_vdw_refined	0.226
r_nbd_refined	0.208
r_nbd_other	0.208
r_nbtor_refined	0.182
r_xyhbond_nbd_refined	0.167
r_symmetry_hbond_refined	0.167
r_chiral_restr	0.092
r_nbtor_other	0.084
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3183
Nucleic Acid Atoms
Solvent Atoms	556
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building