3F6B | pdb_00003f6b

Crystal structure of benzoylformate decarboxylase in complex with the pyridyl inhibitor PAA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BFD	PDB entry 1BFD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	100 mM Tris-HCl pH 8.5, 150 mM CaCl2, 0.5% v/v MPD (2-methyl-2,4-pentanediol), 22% v/v PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.54	α = 90
b = 96.07	β = 90
c = 137.354	γ = 90

Symmetry
Space Group	I 2 2 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		2008-06-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.0332	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	1.34	50	95.7	0.089	16.911	5.9		120069

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)
	1.34	1.39	85.1		0.61		3.8	10128

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1BFD	1.34	46.08	120069	114737	5750	95.56	0.167	0.163	0.162	0.1619	0.182	0.1806	RANDOM	16.285

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]
0.13			-0.01		-0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.102
r_dihedral_angle_4_deg	12.954
r_dihedral_angle_3_deg	11.879
r_dihedral_angle_1_deg	6.09
r_scangle_it	3.874
r_scbond_it	2.716
r_angle_refined_deg	1.863
r_mcangle_it	1.581
r_mcbond_it	1.133
r_symmetry_hbond_refined	0.358
r_nbtor_refined	0.314
r_nbd_refined	0.209
r_symmetry_vdw_refined	0.164
r_xyhbond_nbd_refined	0.144
r_chiral_restr	0.136
r_bond_refined_d	0.02
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3964
Nucleic Acid Atoms
Solvent Atoms	462
Heterogen Atoms	37

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing