3BDE | pdb_00003bde

Crystal structure of a dabb family protein with a ferredoxin-like fold (mll5499) from mesorhizobium loti maff303099 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	7.9	277	NANODROP, 0.2M Na Acetate, 20.0% PEG 3350, No Buffer pH 7.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2	38.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.669	α = 90
b = 28.415	β = 117.78
c = 76.985	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	ADSC QUANTUM 315	KOHZU: Double crystal Si(111)	2007-10-04	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	0.9537, 0.9797, 0.9796	ALS	8.2.2

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	1.79	29.54	94.5	0.074	0.074	7.8	2.3		20638			18.85

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	73.2		0.465	0.465	1.7	1.6	1153

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	29.54	20637	1063	94.02	0.179	0.177	0.19	0.224	0.24	RANDOM	16.841

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]
-0.24		-0.51	0.38		-0.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.502
r_dihedral_angle_4_deg	26.582
r_dihedral_angle_3_deg	10.166
r_scangle_it	5.631
r_scbond_it	4.36
r_dihedral_angle_1_deg	4.245
r_mcangle_it	2.547
r_mcbond_it	1.935
r_angle_refined_deg	1.62
r_angle_other_deg	1.269
r_mcbond_other	0.447
r_symmetry_vdw_other	0.193
r_nbd_refined	0.178
r_nbtor_refined	0.166
r_symmetry_vdw_refined	0.156
r_nbd_other	0.145
r_xyhbond_nbd_refined	0.102
r_symmetry_hbond_refined	0.093
r_chiral_restr	0.088
r_nbtor_other	0.075
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d	0.004
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1640
Nucleic Acid Atoms
Solvent Atoms	253
Heterogen Atoms	64

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
ADSC	data collection
MOSFLM	data reduction
SHELXD	phasing
SHARP	phasing