4QT3 | pdb_00004qt3

Crystal structure resolution of Plasmodium falciparum FK506 binding domain (FKBP35) in complex with Rapamycin at 1.4A resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VN1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	291	0.1M MMT, 25% PEG1500, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.476	α = 90
b = 50.157	β = 90
c = 57.813	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	PSI PILATUS 6M		2014-06-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.97625	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.4	50.15	99.5			28931	28857	1.8	12

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 (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	2VN1	1.4	37.89	28857	28809	1466	99.33	0.1494	0.1475	0.16	0.1871	0.19	RANDOM	22.098

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]
-0.17			-0.65		0.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.417
r_sphericity_free	24.359
r_dihedral_angle_4_deg	16.24
r_dihedral_angle_3_deg	13.267
r_dihedral_angle_1_deg	6.265
r_sphericity_bonded	5.835
r_rigid_bond_restr	4.501
r_angle_other_deg	2.396
r_mcangle_it	1.935
r_mcbond_it	1.515

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.417
r_sphericity_free	24.359
r_dihedral_angle_4_deg	16.24
r_dihedral_angle_3_deg	13.267
r_dihedral_angle_1_deg	6.265
r_sphericity_bonded	5.835
r_rigid_bond_restr	4.501
r_angle_other_deg	2.396
r_mcangle_it	1.935
r_mcbond_it	1.515
r_mcbond_other	1.496
r_angle_refined_deg	1.342
r_chiral_restr	0.076
r_bond_refined_d	0.007
r_bond_other_d	0.007
r_gen_planes_refined	0.007
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	986
Nucleic Acid Atoms
Solvent Atoms	152
Heterogen Atoms	73

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DNA	data collection
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

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.