3S6M

The structure of a Peptidyl-prolyl cis-trans isomerase from Burkholderia pseudomallei

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	289	50% PEG 400, 0.1M NaAcetate pH 4.5, 200mM Lithium sulfate. Direct cryoprotection, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.657	α = 90
b = 80.657	β = 90
c = 43.338	γ = 120

Symmetry
Space Group	P 63

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	RIGAKU SATURN 944+	VariMax Cu-HF	2011-05-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5418

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	50	98.6	0.112	23.8	4		19225

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	1.65	1.68	94.3		0.174		2.3	924

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2NUL	1.651	23.28	19200	978	98.52	0.1485	0.1467	0.1827	RANDOM	16.5407

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]
-0.11	-0.05		-0.11		0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.823
r_dihedral_angle_4_deg	27.253
r_dihedral_angle_3_deg	11.899
r_dihedral_angle_1_deg	5.74
r_scangle_it	3.93
r_scbond_it	2.284
r_mcangle_it	1.387
r_angle_refined_deg	1.375
r_angle_other_deg	0.904
r_mcbond_it	0.759

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.823
r_dihedral_angle_4_deg	27.253
r_dihedral_angle_3_deg	11.899
r_dihedral_angle_1_deg	5.74
r_scangle_it	3.93
r_scbond_it	2.284
r_mcangle_it	1.387
r_angle_refined_deg	1.375
r_angle_other_deg	0.904
r_mcbond_it	0.759
r_mcbond_other	0.217
r_chiral_restr	0.084
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1244
Nucleic Acid Atoms
Solvent Atoms	156
Heterogen Atoms	18

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.