4J4O | pdb_00004j4o

Crystal structure of FK506 binding domain of plasmodium VIVAX FKBP35 in complex with D44

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3IHZ	PDB ENTRY 3IHZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	291	3.0M AMMONIUM SULPHATE, 0.1M BICINE, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.57	65.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.259	α = 90
b = 68.259	β = 90
c = 74.116	γ = 120

Symmetry
Space Group	P 32 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	IMAGE PLATE	RIGAKU RAXIS IV++	MIRRORS	2011-09-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF

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	1.73	33.5	99.8	0.049	22.4	10.32		21268		2

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	1.73	1.79	99.7		0.187	6.9	7.93

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	PDB ENTRY 3IHZ	1.73	20	20015	1088	99.1	0.179	0.177	0.18	0.215	0.21	RANDOM	22.59

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]
0.02	0.01		0.02		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.307
r_dihedral_angle_4_deg	19.665
r_dihedral_angle_3_deg	11.867
r_dihedral_angle_1_deg	6.508
r_scangle_it	4.491
r_scbond_it	2.607
r_mcangle_it	1.711
r_angle_refined_deg	1.563
r_mcbond_it	0.945
r_chiral_restr	0.109

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.307
r_dihedral_angle_4_deg	19.665
r_dihedral_angle_3_deg	11.867
r_dihedral_angle_1_deg	6.508
r_scangle_it	4.491
r_scbond_it	2.607
r_mcangle_it	1.711
r_angle_refined_deg	1.563
r_mcbond_it	0.945
r_chiral_restr	0.109
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	943
Nucleic Acid Atoms
Solvent Atoms	200
Heterogen Atoms	46

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling

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.