3F6E | pdb_00003f6e

Crystal structure of benzoylformate decarboxylase in complex with the pyridyl inhibitor 3-PKB

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3F6B	PDB entry 3F6B

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
2.38	48.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.09	α = 90
b = 95.807	β = 90
c = 137.324	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	82.8	0.106	11.948	4.5	119460	98867

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	42.2		0.7		3.7	5009

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3F6B	1.34	41.31	98826	4897	82.73	0.191	0.19	0.212	0.2266	RANDOM	15.556

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]
0.09			0.02		-0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.077
r_dihedral_angle_4_deg	12.569
r_dihedral_angle_3_deg	11.988
r_dihedral_angle_1_deg	6.32
r_scangle_it	4.186
r_scbond_it	2.869
r_angle_refined_deg	2.017
r_mcangle_it	1.672
r_mcbond_it	1.243
r_nbtor_refined	0.312
r_nbd_refined	0.213
r_symmetry_vdw_refined	0.182
r_symmetry_hbond_refined	0.152
r_xyhbond_nbd_refined	0.147
r_chiral_restr	0.14
r_bond_refined_d	0.024
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3964
Nucleic Acid Atoms
Solvent Atoms	461
Heterogen Atoms	37

Software

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