2OD5 | pdb_00002od5

CRYSTAL STRUCTURE OF A PUTATIVE NUCLEIC ACID BINDING PROTEIN (JCVI_PEP_1096688149193) FROM UNCULTURED MARINE ORGANISM AT 1.79 A RESOLUTION

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP, NANODROP	7	277	1.0M LiCl, 20.0% PEG-6000, 0.1M HEPES pH 7.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.02	59.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.406	α = 90
b = 64.406	β = 90
c = 133.246	γ = 120

Symmetry
Space Group	P 62 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	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2006-11-19	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837, 0.97971	SSRL	BL11-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.6	28.989	100	0.137	0.137	3.9	13.6		16175

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.79	1.84	100		0.017	1.674	0.4	14	1154

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	1.79	28.989	16127	809	99.93	0.19	0.189	0.2	0.213	0.21	RANDOM	31.725

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]
-0.02	-0.01		-0.02		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.394
r_dihedral_angle_3_deg	12.595
r_scangle_it	6.743
r_dihedral_angle_1_deg	5.664
r_scbond_it	5.253
r_dihedral_angle_4_deg	4.303
r_mcangle_it	3.437
r_mcbond_it	2.378
r_angle_refined_deg	1.418
r_angle_other_deg	0.954
r_mcbond_other	0.529
r_symmetry_vdw_other	0.309
r_symmetry_vdw_refined	0.253
r_symmetry_hbond_refined	0.235
r_nbd_refined	0.227
r_nbd_other	0.198
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.148
r_chiral_restr	0.093
r_nbtor_other	0.087
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	720
Nucleic Acid Atoms
Solvent Atoms	77
Heterogen Atoms	45

Software

Software
Software Name	Purpose
MolProbity	model building
SOLVE	phasing
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling