3LZR | pdb_00003lzr

Crystal Structure Analysis of Manganese treated P19 protein from Campylobacter jejuni at 2.73 A at pH 9 and Manganese peak wavelength (1.893 A)

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 Angs 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
2.15	42.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.499	α = 90
b = 73.797	β = 90
c = 75.217	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 325 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	1.893	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	2.73	19.26	92.6	0.015	61.9	3.8		7756	-3	-3	23.6

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)
	2.73	2.88	78		0.019	47.3	3.6	926

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	P6222 incomplete SeMAD model at 2.8 Angs resolution.	2.73	19.26	7400	356	91.84	0.19699	0.1946	0.19	0.24532	0.24	RANDOM	36.236

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]
-0.64			0.89		-0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.55
r_dihedral_angle_3_deg	11.6
r_dihedral_angle_4_deg	10.864
r_dihedral_angle_1_deg	4.929
r_scangle_it	2.581
r_scbond_it	1.535
r_angle_other_deg	1.489
r_mcangle_it	1.044
r_angle_refined_deg	0.91
r_mcbond_it	0.515

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.55
r_dihedral_angle_3_deg	11.6
r_dihedral_angle_4_deg	10.864
r_dihedral_angle_1_deg	4.929
r_scangle_it	2.581
r_scbond_it	1.535
r_angle_other_deg	1.489
r_mcangle_it	1.044
r_angle_refined_deg	0.91
r_mcbond_it	0.515
r_chiral_restr	0.057
r_mcbond_other	0.051
r_bond_refined_d	0.005
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2470
Nucleic Acid Atoms
Solvent Atoms	56
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.