5ECF | pdb_00005ecf

Ligand binding domain 1 of Penicillium marneffei MP1 protein complexed with arachidonic acids

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5E7X

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
2.31	46.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.675	α = 90
b = 104.274	β = 97.44
c = 108.103	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	PIXEL	DECTRIS PILATUS 6M		2013-06-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.99187	SOLEIL	PROXIMA 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	2.6	50	94.4	0.074	8.7	3.6		42305

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	2.6	2.69	69.7		0.39		2.8	3114

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	5E7X	2.6	50	40029	2129	94.57	0.2577	0.2559	0.25	0.2901	0.29	RANDOM	38.161

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]
5.11		-0.21	-1.94		-3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.694
r_dihedral_angle_4_deg	17.975
r_dihedral_angle_3_deg	17.771
r_dihedral_angle_1_deg	4.26
r_angle_other_deg	1.468
r_angle_refined_deg	1.073
r_chiral_restr	0.066
r_bond_refined_d	0.017
r_bond_other_d	0.017
r_gen_planes_refined	0.017

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.694
r_dihedral_angle_4_deg	17.975
r_dihedral_angle_3_deg	17.771
r_dihedral_angle_1_deg	4.26
r_angle_other_deg	1.468
r_angle_refined_deg	1.073
r_chiral_restr	0.066
r_bond_refined_d	0.017
r_bond_other_d	0.017
r_gen_planes_refined	0.017
r_gen_planes_other	0.016

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10917
Nucleic Acid Atoms
Solvent Atoms	19
Heterogen Atoms	88

Software

Software
Software Name	Purpose
DENZO	data collection
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.