3FSJ | pdb_00003fsj

Crystal structure of benzoylformate decarboxylase in complex with the inhibitor MBP

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
2.38	48.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.484	α = 90
b = 95.354	β = 90
c = 137.139	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	Adjustable focusing mirrors in K-B geometry	2006-11-13	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	1.37	50		0.04	41.7	7.5		111618		2	17.7

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)
	1.37	1.41			0.27	7.9	7.3	10367

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	1.37	30.98	111618	109983	11021	98.54	0.163	0.161	0.159	0.1577	0.171	0.1699	RANDOM	11.659

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]
0.03			-0.02		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.082
r_dihedral_angle_4_deg	12.556
r_dihedral_angle_3_deg	11.731
r_dihedral_angle_1_deg	5.773
r_scangle_it	2.206
r_scbond_it	1.491
r_angle_refined_deg	1.214
r_mcangle_it	0.861
r_mcbond_it	0.535
r_nbtor_refined	0.305
r_nbd_refined	0.193
r_symmetry_vdw_refined	0.155
r_symmetry_hbond_refined	0.144
r_metal_ion_refined	0.142
r_xyhbond_nbd_refined	0.103
r_chiral_restr	0.078
r_bond_refined_d	0.006
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3940
Nucleic Acid Atoms
Solvent Atoms	485
Heterogen Atoms	40

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling