3LZN | pdb_00003lzn

Crystal Structure Analysis of the apo P19 protein from Campylobacter jejuni at 1.59 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 ANGS RESOLUTION.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	298	PROTEIN TREATED WITH 30X EXCESS OF EDTA; WASHED, PRECIPITANT WAS 25-45% POLYETHYLENE GLYCOL (PEG) 350, 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
2.11	41.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.396	α = 90
b = 73.037	β = 90
c = 74.817	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	MARMOSAIC 325 mm CCD	Rh coated flat mirror, toroidal focusing mirror, Si 111 monochromator	2007-05-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	1.282	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	1.59	19.11	98.9	0.037	16.6	3.7		40227	-3	-3	29.6

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)
	1.59	1.68	98.6		0.655	2.2	3.7	5772

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.	1.59	18.38	38270	1954	98.72	0.14366	0.14158	0.15	0.18413	0.19	RANDOM	23.712

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]
-0.69			1.22		-0.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.544
r_dihedral_angle_4_deg	15.929
r_dihedral_angle_3_deg	13.413
r_scangle_it	8.175
r_dihedral_angle_1_deg	6.792
r_scbond_it	5.977
r_mcangle_it	3.851
r_mcbond_it	2.636
r_rigid_bond_restr	2
r_angle_other_deg	1.478

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.544
r_dihedral_angle_4_deg	15.929
r_dihedral_angle_3_deg	13.413
r_scangle_it	8.175
r_dihedral_angle_1_deg	6.792
r_scbond_it	5.977
r_mcangle_it	3.851
r_mcbond_it	2.636
r_rigid_bond_restr	2
r_angle_other_deg	1.478
r_angle_refined_deg	1.472
r_mcbond_other	0.894
r_chiral_restr	0.103
r_bond_refined_d	0.014
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	2470
Nucleic Acid Atoms
Solvent Atoms	282
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.