3LZQ | pdb_00003lzq

Crystal Structure Analysis of Manganese treated P19 protein from Campylobacter jejuni at 1.41 A at pH 9

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		P6222 incomplete SeMAD model at 2.8 A resolution.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	298	50% POLYETHYLENE GLYCOL (PEG) 250, 0.1 M CHES (2-(N-CYCLOHEXYLAMINO) ETHANE SULFONIC ACID) BUFFER PH 9.0, CRYO FROZEN WITHOUT ANY ADDITION, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.357	α = 90
b = 73.619	β = 90
c = 75.049	γ = 90

Symmetry
Space Group	P 21 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	CCD	MARMOSAIC 300 mm CCD	Rh coated flat mirror, toroidal focusing mirror, Si 111 monochromator	2006-11-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.979	SSRL	BL9-2

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	1.41	19.21	93.1	0.028	22	4		54201	-3	-3	24

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)
	1.41	1.49	76.8		0.383	3.1	3.8	6391

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 (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	P6222 incomplete SeMAD model at 2.8 A resolution.	1.41	19.21	54201	51527	2674	92.54	0.16889	0.16688	0.18	0.20822	0.22	RANDOM	21.28

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]
-1.2			2.7		-1.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.853
r_dihedral_angle_3_deg	12.878
r_dihedral_angle_4_deg	12.663
r_scangle_it	7.678
r_dihedral_angle_1_deg	6.707
r_scbond_it	5.858
r_mcangle_it	3.814
r_mcbond_it	2.729
r_rigid_bond_restr	2.098
r_angle_other_deg	1.825

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.853
r_dihedral_angle_3_deg	12.878
r_dihedral_angle_4_deg	12.663
r_scangle_it	7.678
r_dihedral_angle_1_deg	6.707
r_scbond_it	5.858
r_mcangle_it	3.814
r_mcbond_it	2.729
r_rigid_bond_restr	2.098
r_angle_other_deg	1.825
r_angle_refined_deg	1.549
r_mcbond_other	0.953
r_chiral_restr	0.099
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2465
Nucleic Acid Atoms
Solvent Atoms	314
Heterogen Atoms	14

Software

Software
Software Name	Purpose
Blu-Ice	data collection
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.