7O60 | pdb_00007o60

Crystal structure of human myelin protein P2 at room temperature from joint X-ray and neutron refinement.

X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		281	28% PEG 6000, 0.1 M citrate, pD 4.75

Crystal Properties
Matthews coefficient	Solvent content
2.82	56.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.952	α = 90
b = 57.952	β = 90
c = 100.79	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	neutron	292	AREA DETECTOR	LADI III		2014-09-02	L	LAUE
2	1	x-ray	293	IMAGE PLATE	MAR scanner 345 mm plate		2016-05-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	NUCLEAR REACTOR	ILL BEAMLINE LADI III	3.0-3.9	ILL	LADI III
2	SEALED TUBE	Xenocs GeniX 3D Cu HF	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	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
2	2	15	98.9		0.06	0.063		0.999		25.2	9.7		12464			27.66
1	2.4	40	60.1		0.189					6.1	4.2		4232			27.66

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
2	2	2.06			0.431	0.513		0.849		3	3.2
1	2.4	2.53			0.304					2.8	2.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	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	2	14.53		1.34		12443	1246	98.97		0.1596	0.1546	0.16	0.2032	0.21		18.85
NEUTRON DIFFRACTION	MOLECULAR REPLACEMENT	2.4	40				4227		58.9		0.2995	0.2947		0.3412

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	17.656
f_angle_d	2.0852
f_chiral_restr	0.104
f_bond_d	0.0292
f_plane_restr	0.0129

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1048
Nucleic Acid Atoms
Solvent Atoms	105
Heterogen Atoms	31

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	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.