3LZO | pdb_00003lzo

Crystal Structure Analysis of the copper-reconstituted P19 protein from Campylobacter jejuni at 1.65 A at pH 10.0

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	10	298	25-45% POLYETHYLENE GLYCOL (PEG) 350, 0.1 M CHES (2-(N-CYCLOHEXYLAMINO) ETHANE SULFONIC ACID) BUFFER PH 10.0, CRYO FROZEN WITHOUT ANY ADDITION, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.831	α = 90
b = 72.581	β = 90
c = 78.817	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	ADSC QUANTUM 315r	Rh coated flat mirror, Si(111) side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg.	2009-04-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	0.979	SSRL	BL7-1

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	1.65	19.34	99.5	0.04	20.2	4.7		39217	-3	-3	29.8

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)
	1.65	1.74	98.7		0.661	2.4	4.7	5597

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.	1.65	19.34	37316	1901	99.48	0.14118	0.13887	0.15	0.18685	0.2	RANDOM	24.981

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]
-0.62			1.29		-0.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.774
r_dihedral_angle_4_deg	19.186
r_dihedral_angle_3_deg	14.525
r_scangle_it	8.562
r_dihedral_angle_1_deg	6.66
r_scbond_it	6.554
r_mcangle_it	4.189
r_mcbond_it	2.908
r_rigid_bond_restr	2.193
r_angle_refined_deg	1.523

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.774
r_dihedral_angle_4_deg	19.186
r_dihedral_angle_3_deg	14.525
r_scangle_it	8.562
r_dihedral_angle_1_deg	6.66
r_scbond_it	6.554
r_mcangle_it	4.189
r_mcbond_it	2.908
r_rigid_bond_restr	2.193
r_angle_refined_deg	1.523
r_mcbond_other	0.893
r_angle_other_deg	0.885
r_chiral_restr	0.098
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2480
Nucleic Acid Atoms
Solvent Atoms	291
Heterogen Atoms	12

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.