6JL9

Crystal structure of a frog ependymin related protein

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	0.2M Calcium acetate hydrate, 0.1M Sodium cacodylate trihydrate pH 6.5, 18%(w/v) Polyethylene glycol 8,000

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.208	α = 90
b = 61.208	β = 90
c = 236.196	γ = 120

Symmetry
Space Group	P 65 2 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	ADSC QUANTUM 270		2018-07-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 7A (6B, 6C1)	1.540	PAL/PLS	7A (6B, 6C1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	53.01	99.7	70.5	19.8		18642

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.03

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	2	53.01	17685	952	99.67	0.19819	0.1942	0.27753	RANDOM	55.467

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]
0.95	0.48		0.95		-3.08

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	37.313
r_dihedral_angle_2_deg	35.918
r_sphericity_bonded	28.537
r_dihedral_angle_4_deg	18.925
r_dihedral_angle_3_deg	16.541
r_long_range_B_refined	13.967
r_long_range_B_other	13.941
r_scangle_other	12.952
r_scbond_it	11.361
r_scbond_other	11.355
r_mcangle_it	11.344
r_mcangle_other	11.338
r_mcbond_it	10.002
r_mcbond_other	9.99
r_dihedral_angle_1_deg	7.567
r_rigid_bond_restr	5.132
r_angle_refined_deg	1.74
r_angle_other_deg	1.473
r_chiral_restr	0.103
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1554
Nucleic Acid Atoms
Solvent Atoms	55
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
ARP/wARP	model building
PHENIX	phasing