3VAW | pdb_00003vaw

Crystal structure of a smt fusion peptidyl-prolyl cis-trans isomerase with surface mutation v3i from burkholderia pseudomallei complexed with fk506

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3UQA	pdb entry 3uqa

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	290	Internal tracking number 226593. PACT well H3. 0.2M Sodium Iodide, 0.1M Bis-Tris Propane, pH 8.5, 20.0% w/v PEG3350, 30% PEG400 Cryo. BupsA.00130.a.D24 PD00194 19.6mg/ml., vapor diffusion, sitting drop, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
1.71	27.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 30.94	α = 90
b = 31.38	β = 95.03
c = 81.26	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		2011-11-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	0.9774	ALS	5.0.1

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	1.55	40.47	97.3	0.036	24.33	3.88	22924	22306	-3	-3	19.899

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	1.55	1.59	70.5		0.151	4.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	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	MR	THROUGHOUT	pdb entry 3uqa	1.55	40.47	2	22924	22298	1148	97.3	0.166	0.166	0.164	0.17	0.194	0.2	RANDOM	14.153

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]
0.85		-0.15	-0.08		-0.8

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.115
r_dihedral_angle_4_deg	17.318
r_dihedral_angle_3_deg	12.291
r_dihedral_angle_1_deg	6.198
r_angle_refined_deg	1.58
r_angle_other_deg	0.871
r_chiral_restr	0.091
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.115
r_dihedral_angle_4_deg	17.318
r_dihedral_angle_3_deg	12.291
r_dihedral_angle_1_deg	6.198
r_angle_refined_deg	1.58
r_angle_other_deg	0.871
r_chiral_restr	0.091
r_bond_refined_d	0.012
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	1395
Nucleic Acid Atoms
Solvent Atoms	154
Heterogen Atoms	57

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
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.