3C1A | pdb_00003c1a

Crystal structure of a putative oxidoreductase (ZP_00056571.1) from Magnetospirillum magnetotacticum MS-1 at 1.85 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	NANODROP, 19.6% PEG 3350, 0.15M Di-ammonium tartrate, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.658	α = 90
b = 86.361	β = 90
c = 87.907	γ = 90

Symmetry
Space Group	P 21 21 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 300 mm CCD	Adjustable focusing mirrors in K-B geometry	2007-10-26	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.91840, 0.97953, 0.97939	APS	23-ID-D

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	1.85	29.988	99.7	0.145	0.145	7.7	3.6		61976			16.379

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	1.85	1.9	98.5		0.885	0.885	2	3.5	4492

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	1.85	29.988	61925	3136	99.6	0.216	0.214	0.22	0.256	0.26	RANDOM	15.499

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]
-1.02			2.3		-1.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.984
r_dihedral_angle_4_deg	19.426
r_dihedral_angle_3_deg	12.619
r_scangle_it	6.828
r_dihedral_angle_1_deg	6.017
r_scbond_it	4.87
r_mcangle_it	2.895
r_mcbond_it	2.06
r_angle_refined_deg	1.503
r_angle_other_deg	0.96
r_mcbond_other	0.626
r_symmetry_vdw_other	0.266
r_symmetry_vdw_refined	0.246
r_nbd_refined	0.216
r_nbd_other	0.198
r_symmetry_hbond_refined	0.18
r_xyhbond_nbd_refined	0.171
r_nbtor_refined	0.17
r_chiral_restr	0.091
r_nbtor_other	0.089
r_xyhbond_nbd_other	0.081
r_bond_refined_d	0.015
r_gen_planes_refined	0.005
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4476
Nucleic Acid Atoms
Solvent Atoms	644
Heterogen Atoms	30

Software

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