2WEX | pdb_00002wex

Crystal structure of human apoM in complex with glycerol 1- myristic acid

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.2		ABOUT 1-2 MICROL OF PROTEIN (10-16 MG/ML IN 20 MM TRIS-HCL, PH 7.2) WERE MIXED WITH 1-2 MICROL OF 30 % PEG1500 (W/V, IN DEIONISED WATER) AND EQUILIBRATED AGAINST 700 MICROL OF RESERVOIR SOLUTION CONTAINING 30 % PEG1500.

Crystal Properties
Matthews coefficient	Solvent content
2.39	47.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.82	α = 90
b = 49.82	β = 90
c = 145.48	γ = 90

Symmetry
Space Group	P 43 21 2

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	RAYONIX			M	SINGLE WAVELENGTH

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

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	20	99.7	0.05	23.53	8.41		13097		3	42.3

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	2.12	99.7		0.54	4.11	8.49

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 2WEW	2	19	12429	654	100	0.21075	0.20831	0.22	0.25708	0.26	RANDOM	19.847

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]
-1.8			-1.8		3.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.487
r_dihedral_angle_4_deg	19.787
r_dihedral_angle_3_deg	18.381
r_dihedral_angle_1_deg	7.02
r_scangle_it	3.614
r_scbond_it	2.606
r_angle_refined_deg	1.8
r_mcangle_it	1.527
r_mcbond_it	1.047
r_symmetry_hbond_refined	0.33
r_nbtor_refined	0.306
r_nbd_refined	0.233
r_symmetry_vdw_refined	0.214
r_xyhbond_nbd_refined	0.185
r_chiral_restr	0.124
r_bond_refined_d	0.018
r_gen_planes_refined	0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1253
Nucleic Acid Atoms
Solvent Atoms	78
Heterogen Atoms	25

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing