4Q4F

Crystal structure of LIMP-2 (space group C2)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	294	30 %w/v Polyethylene Glycol 8000, 0.2 M Ammonium Sulphate, 0.1 M Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
3.33	63.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.686	α = 90
b = 63.386	β = 102.27
c = 114.375	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	PIXEL	PSI PILATUS 6M		2012-07-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.9686	Diamond	I24

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	2.8	50	96.2	0.119	7.1	2.5		15244		-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	2.8	2.9	91.5		0.378	1.8	2.1

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 4Q4B	2.8	50	14450	763	93.93	0.21979	0.21727	0.26957	RANDOM	71.184

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]
0.83		1.62	-2.76		1.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.843
r_dihedral_angle_3_deg	14.222
r_dihedral_angle_4_deg	12.789
r_dihedral_angle_1_deg	5.439
r_long_range_B_refined	3.798
r_long_range_B_other	3.798
r_scangle_other	2.461
r_mcangle_other	2.015
r_mcangle_it	1.938
r_scbond_other	1.438
r_scbond_it	1.323
r_angle_refined_deg	1.232
r_mcbond_it	1.142
r_mcbond_other	1.139
r_angle_other_deg	0.708
r_chiral_restr	0.065
r_bond_refined_d	0.005
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3191
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	377

Software

Software
Software Name	Purpose
GDA	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling