3N0V | pdb_00003n0v

Crystal structure of a formyltetrahydrofolate deformylase (PP_0327) from PSEUDOMONAS PUTIDA KT2440 at 2.25 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP		277	0.1860M potassium fluoride 20.4000% polyethylene glycol 3350, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
2	VAPOR DIFFUSION,SITTING DROP,NANODROP	8	277	10.0000% PEG-8000, 0.1M Imidazole pH 8.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.213	α = 90
b = 93.965	β = 101.38
c = 97.129	γ = 90

Symmetry
Space Group	P 1 21 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 325 mm CCD	Flat mirror (vertical focusing)	2010-02-11	M	MAD
2	1	x-ray	100	CCD	MARMOSAIC 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2009-07-31	M	MAD
,0.97908	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.95369	SSRL	BL11-1
2	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97922,0.91837	SSRL	BL9-2
,0.97908

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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
1,2	2.25	42.133	99.8	0.109		3.1		67847			41.528

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	2.25	42.133	67821	3426	99.77	0.225	0.222	0.23	0.274	0.28	RANDOM	64.366

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]
-0.57		-0.22	0.31		0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.612
r_dihedral_angle_4_deg	16.156
r_dihedral_angle_3_deg	12.364
r_dihedral_angle_1_deg	5.809
r_angle_refined_deg	1.046
r_angle_other_deg	0.811
r_chiral_restr	0.065
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.612
r_dihedral_angle_4_deg	16.156
r_dihedral_angle_3_deg	12.364
r_dihedral_angle_1_deg	5.809
r_angle_refined_deg	1.046
r_angle_other_deg	0.811
r_chiral_restr	0.065
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8947
Nucleic Acid Atoms
Solvent Atoms	421
Heterogen Atoms

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.