4G2P | pdb_00004g2p

Crystal structure of peptidyl-prolyl cis-trans isomerase domain II of molecular chaperone SurA from Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1M5Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	297	0.2M Lithium sulfate, 0.1M Bis-Tris, 25% PEG3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.499	α = 90
b = 39.611	β = 101.7
c = 68.581	γ = 90

Symmetry
Space Group	P 1 21 1

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		2011-04-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97921	APS	19-ID

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	1.82	50	98.8	0.084	34.3	4.4	20735	20486		-3

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	1.82	1.85	90.6		0.389	3.7	3.2	930

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 (All)	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	1M5Y	1.82	50	20476	20476	1052	98.57	0.1652	0.1652	0.1612	0.16	0.2381	0.24	RANDOM	39.0817

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]
1.27		-5.04	-3.99		0.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.561
r_sphericity_free	36.799
r_sphericity_bonded	23.617
r_dihedral_angle_3_deg	14.039
r_dihedral_angle_1_deg	6.435
r_dihedral_angle_4_deg	6.435
r_rigid_bond_restr	3.572
r_angle_refined_deg	1.433
r_chiral_restr	0.09
r_bond_refined_d	0.011

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.561
r_sphericity_free	36.799
r_sphericity_bonded	23.617
r_dihedral_angle_3_deg	14.039
r_dihedral_angle_1_deg	6.435
r_dihedral_angle_4_deg	6.435
r_rigid_bond_restr	3.572
r_angle_refined_deg	1.433
r_chiral_restr	0.09
r_bond_refined_d	0.011
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1660
Nucleic Acid Atoms
Solvent Atoms	186
Heterogen Atoms	22

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MOLREP	phasing
Coot	model building

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.