4F8P | pdb_00004f8p

X-ray structure of PsaA from Yersinia pestis, in complex with galactose

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	298	1.4 M Sodium Formate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.12	60.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.266	α = 90
b = 59.266	β = 90
c = 200.088	γ = 120

Symmetry
Space Group	P 65

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 300 mm CCD		2010-11-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1	APS	22-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	2.05	50	91.7	0.09	14.8	4.7		22657

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	2.07	2.14	72.8		0.562		1.7	1779

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	MOLECULAR REPLACEMENT	THROUGHOUT	2.05	25	22654	1158	91.75	0.2453	0.2434	0.25	0.2787	0.28	RANDOM	50.2723

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]
1.92	0.96		1.92		-2.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.187
r_dihedral_angle_3_deg	21.51
r_scangle_it	9.121
r_dihedral_angle_4_deg	8.701
r_dihedral_angle_1_deg	7.587
r_scbond_it	6.522
r_mcangle_it	5.467
r_angle_other_deg	5.178
r_mcbond_it	3.553
r_angle_refined_deg	1.724
r_chiral_restr	0.11
r_bond_other_d	0.067
r_mcbond_other	0.033
r_bond_refined_d	0.018
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2224
Nucleic Acid Atoms
Solvent Atoms	49
Heterogen Atoms	44

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection