3EY6 | pdb_00003ey6

Crystal structure of the FK506-binding domain of human FKBP38

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	30% PEG 4000, 0.2M calcium chloride, 0.1M TRIS, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.05	39.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 29.057	α = 90
b = 60.288	β = 97.59
c = 30.84	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	93	CCD	MARMOSAIC 225 mm CCD	mirrors	2006-06-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.9537	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.05	30.5	90.4	0.038	0.038	11.709	3.4		44414	2	2	9.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.05	1.11	52.3		0.114	0.114	5.9	2.1	3735

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 (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 2AWG	1.05	30.5	44414	44413	2242	90.43	0.136	0.136	0.135	0.1364	0.161	0.1627	RANDOM	10.235

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]
0.22		0.37	-0.31		0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.275
r_dihedral_angle_4_deg	24.396
r_dihedral_angle_3_deg	9.861
r_dihedral_angle_1_deg	7.207
r_sphericity_free	5.796
r_sphericity_bonded	3.595
r_scangle_it	3.108
r_mcangle_it	2.419
r_scbond_it	2.174
r_mcbond_it	1.618
r_angle_refined_deg	1.545
r_rigid_bond_restr	1.27
r_chiral_restr	0.099
r_bond_refined_d	0.01
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	888
Nucleic Acid Atoms
Solvent Atoms	244
Heterogen Atoms

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection