2OP5 | pdb_00002op5

CRYSTAL STRUCTURE OF A DIMERIC FERREDOXIN-LIKE PROTEIN (JCVI_PEP_1096672785533) FROM UNCULTURED MARINE ORGANISM AT 2.20 A RESOLUTION

X-RAY DIFFRACTION

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Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.558	α = 90
b = 84.629	β = 90
c = 144.952	γ = 90

Symmetry
Space Group	P 21 21 21

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	2006-10-20	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.94645, 0.97942, 0.97921	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	2.2	48.34	99.6	0.15	7.22			36082			25.76

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	2.2	2.28	98.8		0.683	1.8		3630

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 (All)	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	2.2	48.34	36027	1799	99.67	0.233	0.233	0.23	0.23	0.292	0.3	RANDOM	27.408

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]
0.43			1.26		-1.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.52
r_dihedral_angle_4_deg	16.868
r_dihedral_angle_3_deg	11.613
r_dihedral_angle_1_deg	3.367
r_scangle_it	2.561
r_scbond_it	1.764
r_angle_refined_deg	1.51
r_mcangle_it	1.371
r_mcbond_it	0.904
r_angle_other_deg	0.863
r_mcbond_other	0.211
r_xyhbond_nbd_refined	0.195
r_symmetry_hbond_refined	0.192
r_nbd_refined	0.183
r_nbtor_refined	0.183
r_nbd_other	0.158
r_symmetry_vdw_other	0.151
r_symmetry_vdw_refined	0.144
r_chiral_restr	0.085
r_nbtor_other	0.085
r_xyhbond_nbd_other	0.028
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5307
Nucleic Acid Atoms
Solvent Atoms	161
Heterogen Atoms	36

Software

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