3OBI

Crystal structure of a formyltetrahydrofolate deformylase (NP_949368) from RHODOPSEUDOMONAS PALUSTRIS CGA009 at 1.95 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	277	20.0% polyethylene glycol 8000, 0.3M calcium acetate, 0.1M sodium cacodylate pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.76	55.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.048	α = 90
b = 141.111	β = 107.83
c = 77.563	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 collimating mirror, toroid focusing mirror	2010-05-13	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.90497,0.97939,0.97915	SSRL	BL9-2

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	1.95	29.673	97.2	0.108	6.6	3.5	101081	101081			20.735

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	1.95	2	94.1		0.583	0.583	1.3	3.5	7180

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.95	29.673	101028	5035	97.07	0.2358	0.2336	0.278	RANDOM	30.989

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]
0.62		-0.38	-0.13		-0.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.699
r_dihedral_angle_4_deg	13.278
r_dihedral_angle_3_deg	11.042
r_dihedral_angle_1_deg	3.944
r_scangle_it	3.359
r_scbond_it	2.033
r_angle_refined_deg	1.663
r_mcangle_it	1.377
r_angle_other_deg	1.281
r_mcbond_it	0.751

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.699
r_dihedral_angle_4_deg	13.278
r_dihedral_angle_3_deg	11.042
r_dihedral_angle_1_deg	3.944
r_scangle_it	3.359
r_scbond_it	2.033
r_angle_refined_deg	1.663
r_mcangle_it	1.377
r_angle_other_deg	1.281
r_mcbond_it	0.751
r_mcbond_other	0.167
r_chiral_restr	0.099
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9085
Nucleic Acid Atoms
Solvent Atoms	1001
Heterogen Atoms	116

Software

Software
Software Name	Purpose
SHELX	phasing
REFMAC	refinement
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.