3BY7 | pdb_00003by7

CRYSTAL STRUCTURE OF A PROTEIN STRUCTURALLY SIMILAR TO SM/LSM-LIKE RNA-BINDING PROTEINS (JCVI_PEP_1096686650277) FROM UNCULTURED MARINE ORGANISM AT 2.60 A RESOLUTION

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.3	277	NANODROP, 0.2M Ca Acetate, 20.0% PEG 3350, No Buffer pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.25	α = 90
b = 77.18	β = 113.82
c = 71.47	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	CCD	MARMOSAIC 300 mm CCD	Adjustable focusing mirrors in K-B geometry	2007-08-19	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.95373, 0.97957, 0.97942	APS	23-ID-D

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	2.6	27.057	95.7	0.047	9.46			16122		-3	58.562

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	2.6	2.69	92.4		0.404	1.8

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.6	27.057	16120	825	96.58	0.238	0.235	0.24	0.285	0.28	RANDOM	32.898

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]
-0.18		-0.3	4.18		-4.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.758
r_dihedral_angle_3_deg	16.684
r_dihedral_angle_4_deg	13.625
r_dihedral_angle_1_deg	6.42
r_scangle_it	3.747
r_scbond_it	2.381
r_angle_refined_deg	1.247
r_mcangle_it	1.027
r_angle_other_deg	0.871
r_mcbond_it	0.785
r_mcbond_other	0.268
r_symmetry_hbond_refined	0.242
r_symmetry_vdw_other	0.233
r_nbd_refined	0.198
r_nbd_other	0.192
r_nbtor_refined	0.175
r_xyhbond_nbd_refined	0.162
r_symmetry_vdw_refined	0.125
r_nbtor_other	0.083
r_chiral_restr	0.072
r_bond_refined_d	0.013
r_bond_other_d	0.005
r_gen_planes_refined	0.004
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3024
Nucleic Acid Atoms
Solvent Atoms	7
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing