5J7R

2.5 Angstrom Crystal Structure of Putative Lipoprotein from Clostridium perfringens

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	292	Protein: 16.8 mg/ml, 0.1M Tris HCl (pH 8.3); Screen: JCSG+ (H11), 0.2M Magnesium chloride, 0.1M Bis-Tris pH 5.5, 25% (w/v) PEG 3350.

Crystal Properties
Matthews coefficient	Solvent content
2	38.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.212	α = 90
b = 118.212	β = 90
c = 71.836	γ = 120

Symmetry
Space Group	P 32 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	CCD	MARMOSAIC 225 mm CCD	C(111)	2016-03-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	CC (Half)	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	2.5	29.55	99.9	0.064	0.064	0.905	49.7	9.2		20303		-3	69.4

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	2.5	2.54	100		0.618	4.3	9.5

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	2.5	29.55	19217	1068	99.74	0.22126	0.21885	0.26771	RANDOM	82.761

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]
-0.2	-0.1		-0.2		0.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.249
r_dihedral_angle_3_deg	10.01
r_long_range_B_refined	8.598
r_long_range_B_other	8.539
r_scangle_other	5.701
r_mcangle_it	4.777
r_mcangle_other	4.776
r_scbond_it	3.589
r_scbond_other	3.585
r_mcbond_it	2.993
r_mcbond_other	2.985
r_dihedral_angle_1_deg	1.628
r_angle_refined_deg	1.601
r_angle_other_deg	1.517
r_chiral_restr	0.09
r_gen_planes_refined	0.022
r_gen_planes_other	0.02
r_bond_refined_d	0.01
r_bond_other_d	0.007
r_dihedral_angle_4_deg
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	4458
Nucleic Acid Atoms
Solvent Atoms	81
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing