8ORR | pdb_00008orr

Outer membrane protein assembly factor BamB from Klebsiella pneumoniae

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	22% PEG 400, 0.1 M sodium acetate trihydrate (pH 4.6) and 0.08 M cadmium acetate trihydrate

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.095	α = 90
b = 50.095	β = 90
c = 259.774	γ = 90

Symmetry
Space Group	P 43 21 2

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 2M		2017-02-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9282	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	29.285	99.8	0.073	1	25.6	24		48078

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.57	1.61	97.7		0.665	0.92	3.3

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.68	29.285	39184	1954	99.964	0.173	0.1711	0.18	0.2098	0.22	22.911

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]
0.191			0.191		-0.382

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.281
r_dihedral_angle_3_deg	12.696
r_dihedral_angle_4_deg	12.011
r_dihedral_angle_1_deg	7.215
r_lrange_it	5.745
r_lrange_other	5.536
r_scangle_it	2.952
r_scangle_other	2.951
r_mcangle_it	2.392
r_mcangle_other	2.392
r_scbond_it	1.856
r_scbond_other	1.855
r_mcbond_it	1.45
r_mcbond_other	1.43
r_angle_refined_deg	1.426
r_angle_other_deg	1.271
r_symmetry_nbd_refined	0.274
r_nbd_refined	0.188
r_xyhbond_nbd_refined	0.188
r_metal_ion_refined	0.176
r_symmetry_nbd_other	0.17
r_nbd_other	0.163
r_nbtor_refined	0.144
r_symmetry_xyhbond_nbd_refined	0.137
r_symmetry_nbtor_other	0.07
r_chiral_restr	0.058
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2631
Nucleic Acid Atoms
Solvent Atoms	320
Heterogen Atoms	6

Software

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