4BFC | pdb_00004bfc

Crystal structure of the C-terminal CMP-Kdo binding domain of WaaA from Acinetobacter baumannii

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2XCI	PDB ENTRY 2XCI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6		0.1M NA CITRATE BUFFER PH 6.0, 0.2 MM LITHIUM SULPHATE AND 17 TO 23 % PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
3.46	64.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.37	α = 90
b = 110.37	β = 90
c = 70.34	γ = 120

Symmetry
Space Group	H 3

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	MARRESEARCH MAR165	MIRROR	2012-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I911-3		MAX II	I911-3

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	1.7	30	99.4	0.05	24.9	5.7		35057		3.77

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	1.7	1.8	98.8		0.46	3.77	5.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	PDB ENTRY 2XCI	1.7	28.33	33299	1754	99.38	0.13518	0.13383	0.132	0.16093	0.1531	RANDOM	29.23

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]
-9.83			-9.83		19.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.174
r_dihedral_angle_4_deg	20.105
r_dihedral_angle_3_deg	13.581
r_dihedral_angle_1_deg	6.201
r_angle_refined_deg	1.885
r_angle_other_deg	1.885
r_chiral_restr	0.135
r_bond_refined_d	0.019
r_bond_other_d	0.019
r_gen_planes_refined	0.011
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1532
Nucleic Acid Atoms
Solvent Atoms	186
Heterogen Atoms	13

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing