4DZ2

Crystal structure of a Peptidyl-prolyl cis-trans isomerase with surface mutation R92G from Burkholderia pseudomallei complexed with FK506

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3VAW	PDB entry 3vaw

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	290	Internal tracking number 224744. JCSG well D10. 0.1M Cacodylate pH 6.5, 200mM Calcium Acetate, 30.0% w/v PEG400, 20% Ethylene Glycol Cryo. BupsA.00130.a.D239 PD00214 21.8mg/ml, vapor diffusion, sitting drop, temperature 290K, VAPOR DIFFUSION, SITTING DROP

Crystal Properties
Matthews coefficient	Solvent content
3.09	60.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.44	α = 90
b = 49.05	β = 123.05
c = 66.64	γ = 90

Symmetry
Space Group	C 1 2 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	RIGAKU SATURN 944+		2011-10-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	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	2	44.61	97.5	0.047	26.88	6.44	19744	19250	-3	-3	23.506

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	2	2.05	96.6		0.131	9.1

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MR	THROUGHOUT	PDB entry 3vaw	2	44.61	19744	18755	950	95.29	0.22	0.22	0.219	0.247	RANDOM	21.826

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]
-0.94		-0.35	1.09		-0.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	23.937
r_dihedral_angle_4_deg	21.543
r_dihedral_angle_3_deg	11.77
r_dihedral_angle_1_deg	6.664
r_angle_refined_deg	1.473
r_angle_other_deg	0.89
r_chiral_restr	0.071
r_bond_refined_d	0.015
r_gen_planes_refined	0.005
r_bond_other_d	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	23.937
r_dihedral_angle_4_deg	21.543
r_dihedral_angle_3_deg	11.77
r_dihedral_angle_1_deg	6.664
r_angle_refined_deg	1.473
r_angle_other_deg	0.89
r_chiral_restr	0.071
r_bond_refined_d	0.015
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1650
Nucleic Acid Atoms
Solvent Atoms	237
Heterogen Atoms	116

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

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.