3LZL | pdb_00003lzl

Crystal Structure Analysis of the as-solated P19 protein from Campylobacter jejuni at 1.45 A at pH 9.0

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, CRYOGENIC CONDITION 30% GLYCEROL IN PRECIPITANT MIXTURE, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.533	α = 90
b = 73.545	β = 90
c = 75.06	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	2006-12-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	1.127	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	1.45	19.21	98.6	0.04	14.8	4.4		53633	-3	-3	27.3

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)
	1.45	1.53	97.3		0.517	0.517	2.3	4.3	7657

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 A resolution.	1.45	18.77	50981	2651	98.42	0.14337	0.14115	0.14	0.18668	0.19	RANDOM	23.882

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]
-1.05			2.3		-1.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.689
r_dihedral_angle_4_deg	15.312
r_dihedral_angle_3_deg	11.631
r_scangle_it	10.022
r_scbond_it	7.591
r_dihedral_angle_1_deg	6.714
r_mcangle_it	4.963
r_mcbond_it	3.45
r_rigid_bond_restr	2.611
r_angle_other_deg	2.282

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.689
r_dihedral_angle_4_deg	15.312
r_dihedral_angle_3_deg	11.631
r_scangle_it	10.022
r_scbond_it	7.591
r_dihedral_angle_1_deg	6.714
r_mcangle_it	4.963
r_mcbond_it	3.45
r_rigid_bond_restr	2.611
r_angle_other_deg	2.282
r_angle_refined_deg	1.531
r_mcbond_other	1.419
r_chiral_restr	0.105
r_bond_refined_d	0.017
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2461
Nucleic Acid Atoms
Solvent Atoms	353
Heterogen Atoms	7

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.