5FB7 | pdb_00005fb7

Ligand binding domain 2 of Penicillium marneffei MP1 protein complexed with multiple arachidonic acids

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5CSD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	298	PEG 4000, sodium acetate, ammonium acetate

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.239	α = 90
b = 98.495	β = 90.01
c = 100.12	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	ADSC QUANTUM 315r		2012-03-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.9793	SSRF	BL17U

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	1.5	50	98.9	0.066	13	7.4		90586

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	1.5	1.55	100		0.567		7.1	9161

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	5CSD	1.5	50	86037	4549	98.84	0.1923	0.191	0.1911	0.2169	0.2167	RANDOM	30.275

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]
-0.25		-0.16	-1.55		1.8

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.766
r_dihedral_angle_4_deg	18.058
r_dihedral_angle_3_deg	13.49
r_dihedral_angle_1_deg	4.246
r_mcangle_it	1.77
r_angle_refined_deg	1.432
r_mcbond_it	1.224
r_mcbond_other	1.219
r_angle_other_deg	1.162
r_chiral_restr	0.091
r_bond_refined_d	0.017
r_gen_planes_refined	0.015
r_gen_planes_other	0.009
r_bond_other_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4592
Nucleic Acid Atoms
Solvent Atoms	427
Heterogen Atoms	176

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data collection
SCALEPACK	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
HKL-2000	data reduction