4MMP | pdb_00004mmp

Structure of Sialic Acid Binding Protein from Pasturella Multocida

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3B50	PDB ENTRY 3B50

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	Drops were setup with equal volume of protein and 1.6M Sodium citrate tribasic dihydrate pH 6.5(crystallization buffer) and suspended over 100 l of crystallization buffer, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.643	α = 90
b = 77.758	β = 90
c = 85.519	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	mirrors	2012-02-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.00	APS	17-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.57	85.519	99.4	0.086	13.1	6.2	40313	40313			21.5

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	1.57	1.65	97.1		0.439	0.439	1.7	5.3	5648

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	PDB ENTRY 3B50	1.57	57.53	40313	40254	2016	99.16	0.1635	0.1635	0.1616	0.166	0.1998	0.2009	RANDOM	21.9862

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]
-0.03			-0.25		0.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.548
r_dihedral_angle_3_deg	14.702
r_dihedral_angle_4_deg	7.256
r_dihedral_angle_1_deg	6.203
r_angle_refined_deg	2.131
r_angle_other_deg	1.089
r_chiral_restr	0.13
r_bond_refined_d	0.023
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2410
Nucleic Acid Atoms
Solvent Atoms	193
Heterogen Atoms	21

Software

Software
Software Name	Purpose
SCALA	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
XDS	data reduction